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MINIREVIEW
The social life of ribosomal proteins
Ditlev E. Brodersen and Poul Nissen
Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Denmark
Introduction
Ribosomes are complex macromolecular machines that
are responsible for the production of every protein in
every living cell [1]. Ribosomes are themselves built
from the very molecules of life; protein and RNA, and
ribosomal composition and structure and the inter-
action between the two types of building blocks within
them have always fascinated researchers. In recent lit-
erature there has been renewed focus on rRNA as the
main, and perhaps only, catalyst in the ribosome – a
development which in the minds of many in the field
has left ribosomal proteins in the dark as ‘merely glue’.
In this review we highlight some of the many import-
ant biological roles of ribosomal proteins, apart from
being ‘RNA-glue’, and show that they indeed seem to
have a social life after all.
Until the year 2000, ribosomal protein structure and
interaction with rRNA were mainly studied in a ‘dissect-
ing’ fashion, focusing on each individual protein in turn
[2]. Many individual protein structures were determined
in isolation and their interactions with rRNA were
mapped by various biochemical techniques, such as hyd-
roxy-radical probing, protein footprinting, mutational
analysis and cross-linking [3]. Though these experiments
created a wealth of useful information about the struc-
tural and functional organization of the ribosome, the
information was very ‘local’ in the sense that it focused

on the close surroundings of each ribosomal protein.
The overall structure and inner workings of the ribo-
some therefore remained elusive.
A unified understanding of the ribosome was not
possible until complete atomic structures of the two
subunits that make up the bacterial 70S ribosome, the
50S and 30S subunits, were published in the summer
of 2000 (Fig. 1) [4–6]. Not only did these structures
(1.5 MDa and 850 kDa, respectively) represent the lar-
gest nonsymmetric crystal structures ever determined,
they also increased the size of the nucleic acid database
(NDB; by several orders
of magnitude. The structures contained nothing short
of a goldmine of information about RNA structure
and immediately suggested several important new
RNA folds and rationales of RNA tertiary and quater-
nary structure that had not hitherto been appreciated
[5,7,8]. A wealth of new information about protein–
RNA interactions was likewise deduced from analysis
of the 50 or more proteins in the two subunits, in a
Keywords
crystallography; protein synthesis; ribosomal
proteins structure; ribosome; rRNA;
translation
Correspondence
D. E. Brodersen or P. Nissen, Centre for
Structural Biology, Department of Molecular
Biology, University of Aarhus, Gustav Wieds
Vej 10c, DK-8000 A
˚

rhus C, Denmark
E-mail: or
(Received 25 January 2005, accepted
7 March 2005)
doi:10.1111/j.1742-4658.2005.04651.x
Ribosomal proteins hold a unique position in biology because their func-
tion is so closely tied to the large rRNAs of the ribosomes in all kingdoms
of life. Following the determination of the complete crystal structures of
both the large and small ribosomal subunits from bacteria, the functional
role of the proteins has often been overlooked when focusing on rRNAs as
the catalysts of translation. In this review we highlight some of the many
known and important functions of ribosomal proteins, both during trans-
lation on the ribosome and in a wider context.
Abbreviations
EF-Tu, elongation factor Tu; hnRNP, heteronuclear ribonucleoparticle; IF1, initiation factor 1; IRES, internal ribosome entry site; OB-fold,
oligonucleotide-binding fold; PNPase, polynucleotide phosphorylase; RACK1, receptor of activated C kinase; SRP, signal recognition particle.
2098 FEBS Journal 272 (2005) 2098–2108 ª 2005 FEBS
field which had previously been dominated by more
specialized complexes such as the synthetase–transfer
RNA complexes [9,10].
Ribosomal proteins in the presubunit structure era
From about 1990 until the complete subunit structures
were published in 2000, several research groups invested
significant efforts in determining the structures of
individual ribosomal protein structures [2,11,12]. With
21 proteins in the bacterial 30S and more than 30 in
the 50S subunit, this was not only a gigantic task, but
it also proved exceedingly difficult in many cases.
Obviously, due to their tight interaction with rRNA
in vivo, ribosomal proteins could not always be crystal-

lised in isolation, but in some cases, such as for example
small ribosomal subunit proteins S12 and S4, simply
handling the isolated proteins in vitro proved extremely
difficult (V. Ramakrishnan, MRC-LMB, Cambridge,
UK, personal communication). Today we know that
S9 / S13
tRNA binding
at the P site
S4/S5
ram
mutations
S7
tRNA binding
at the E site
S12
tRNA decoding
at the A site
A
B
L5
P site tRNA
5S RNA
L2 / L3
Peptidyl
transferase
L16 (L10e)
tRNA binding
at the A site
L23 / L24
Exit tunnel

end
L4 / L22
Line peptide
exit tunnel
L1
L1
S1
S11
mRNA binding
at the E site
A P E
E
A
P
Fig. 1. An overview of ribosomal proteins with known functional roles. (A) The bacterial 30S subunit from Thermus thermophilus in back
(left) and front (50S-facing, right) views [5]. The approximate location and extent of ribosomal protein S1 has been indicated by a transparent
green area and is based on [67]. The three tRNA-binding sites, A (aminoacyl), P (peptidyl) and E (exit) are likewise indicated. (B) The archaeal
50S subunit from Haloarcula marismortui in front (30S-facing, left) and back (right) views [4]. The approximate shape and extent of the L1
stalk has been indicated in blue. Figure prepared with
PYMOL [68].
D. E. Brodersen and P. Nissen The social life of ribosomal proteins
FEBS Journal 272 (2005) 2098–2108 ª 2005 FEBS 2099
these problems were caused by long peptide extrusions
(colloquially known as ‘tails’) that many ribosomal
proteins possess (Fig. 2A). Within the ribosome, these
tails often extend away from the main core of the indi-
vidual protein and anchor it to the rRNA. In fact,
some of the more extended ribosomal proteins (such as
S13 or S14) were never crystallised in isolation presum-
ably due to their complete lack of a globular protein

fold (Fig. 2B). Towards the end of the ‘presubunit era’
the first examples of structures of isolated protein–
rRNA complexes representing important subdomains
of the subunits emerged (such as the S15–S6–S18 [13]
and L11–RNA complexes [14]). This strategy, however,
became more difficult with increasing complexity and
finally was made obsolete with the completion of the
entire subunit structures. The L1–RNA complex repre-
sents an important exception [15,16], because this
region was disordered and not determined from the
50S structure [4]. Likewise, the complete structure of
the S1 protein in the 30S remains unknown.
From the increasing set of ribosomal protein struc-
tures it was tempting to try to deduce general ideas
about how ribosomal RNA is recognized in relation to
the variation in protein folds [17]; however, this task
proved very difficult and remained so even after the
complete subunit structures had been determined
[9,10].
Ribosomal proteins in the postsubunit
structure era
Upon the determination of both the complete 30S and
50S ribosomal subunit structures, it immediately
became apparent that ribosomal proteins possessed
features unlike those seen in any other protein struc-
ture to date. Neutron scattering and immunoelectron
microscopy experiments carried out in the 1980s had
already established that most ribosomal proteins are
located at the surface of the particle [18,19], while the
rRNA component seemed to make up the central core.

The atomic resolution crystal structures of the two
subunits were indeed able to confirm most of these
results but they also demonstrated that many proteins
contain long peptide tails, either in their termini or
present as internal, extended loop structures, which
apparently function to anchor each protein to the
RNA core and increase the total interaction surface
with the rRNA (Fig. 2A) [4,5,9,10].
The presence of the extended tails of ribosomal pro-
teins was noticed immediately by researchers working
on both the 50S and 30S subunits and does seem to be
a general feature of ribosomal architecture [4,5]. How-
ever, focus was gathering on the question of how
the ribosome performed its many functions; binding
tRNA, catalysing peptidyl transfer, and the complex
process of translocation. A central point was whether
these functions were carried out by RNA or protein
components. As catalysis was assumed to take place
at internal tRNA-binding sites on the ribosome, the
localization of the proteins on the surface of the parti-
cle could easily mean that they were purely architec-
tural, i.e. being present to shape the rRNA into the
correct tertiary fold for it to carry out its catalytic
function – simply ‘RNA glue’.
Contrary to this, mutational analysis had for many
years ascribed significant functional relevance to sev-
eral ribosomal proteins, such as small ribosomal pro-
tein S12, which was known to be important for
correct decoding of tRNA in the ribosomal A site
(Fig. 1A, Table 1) [20]. Likewise, mutations located in

proteins S4 and S5 in the small subunit appeared to
confer resistance to the antibiotic streptomycin, and
be related to the accuracy of the ribosome and a
Core domain
A
B
Tail
Zn
2+
Fig. 2. Examples of ribosomal protein structure. (A) L44e from the
Haloarcula marismortui 50S subunit has a zinc-binding domain
structure in one end and a long tail in the other. The protein is rain-
bow-coloured from the N- (blue) to C-terminus (red). (B) S14 from
the Thermus thermophilus 30S has no globular protein structure at
all. Figure prepared with
PYMOL [68].
The social life of ribosomal proteins D. E. Brodersen and P. Nissen
2100 FEBS Journal 272 (2005) 2098–2108 ª 2005 FEBS
switch between two internal states known as restrict-
ive and ribosome ambiguity (ram) [21,22]. So the
question was really whether the functional effects of
these mutations were due to the architectural and sta-
bilizing role of the proteins alone, i.e. that perturba-
tion of protein structure would affect the catalytic
activity of the rRNA in an allosteric way, or that the
proteins themselves were somehow involved in cata-
lysis, which certainly had been the dominating hypo-
thesis earlier. Even with most proteins on the surface
of the ribosome, the long-ranging tails observed did
allow in many cases for the latter scenario, in that

they would be able to interact with functional centres
directly. In fact, it was found upon determination of
the subunit structures that many proteins did have
residues rather close to the sites of action. Examples
are S9 and S13, which have tails that come very close
to the P site tRNA in the 30S; L2 and L3, which sta-
bilize the rRNA surrounding the peptidyl transferase
center in the 50S; and L4 and L22 that line the pep-
tide exit tunnel (Fig. 1A). Furthermore, small ribo-
somal subunit protein S12 was found not at the
surface of the ribosome but right at the interface
between the two subunits and hence very close to the
tRNA-binding sites [5].
To improve the understanding of ribosomal func-
tion further, the Steitz group focused on how the
large ribosomal subunit carried out its catalytic func-
tion, the peptidyl transfer reaction [23,24], while the
Ramakrishnan group focused on how the small sub-
unit would bind and decode tRNA in the A site
[25–27]. From the structural analysis of the 50S sub-
unit it immediately became clear that there were no
protein residues near any of the rRNA bases implica-
ted in peptidyl transfer, and the ribosome was quickly
pronounced a ‘ribozyme’ [23]. In the small subunit
the situation was more complicated because protein
S12 was found very close to the decoding site at the
A site. In fact, several amino acids of the protein
were shown to be involved in the recognition process
that leads to acceptance of the correct tRNA at the
site [25]. This challenged the ribozyme idea to some

extent; however, it could be shown that it was pri-
marily the least significant codon–anticodon inter-
action (the ‘wobble’) that was affected by protein
interactions, while the predominant decoding inter-
actions essentially were carried out by universally
conserved bases near the 3¢ end of 16S rRNA (A1492
and A1493 in combination with G530, using Escheri-
chia coli numbering). So the possibility remained that
the ribosome had started its life as an entirely RNA-
catalysed enzyme and only later evolved more special-
ized functions that were protein-dependent.
Ribosomal proteins implicated
in ribosome function
mRNA recognition
In the translating state, the mRNA is tightly wrapped
around the upper part of the 30S subunit (the ‘head’)
and bends twice away from the 70S ribosome, presum-
ably to avoid interference with movements required
during translation (Fig. 3A) [28]. Several ribosomal
proteins, primarily on the small subunit, are respon-
sible for tethering mRNA to the ribosome, most
noticeably S1, S7 and S11. S1 is a highly unusual ribo-
somal protein being more than twice as large as the
second largest protein (S2) and consisting of up to six
repeats of the oligonucleotide-binding fold (OB-fold),
each similar in sequence to translation initiation factor
1 (IF1) and several other RNA-binding proteins such
as transcription factors (reviewed in [29]). S1 is located
on the back of the 30S where it presumably has several
functions, including raising the affinity of the ribosome

for single-stranded RNA in a nonsequence-specific
fashion as well as keeping ‘unused’ parts of the mRNA
away from functionally active parts of the ribosomal
Table 1. Examples of ribosomal proteins with a known function.
Protein Subunit Function
Prokaryotes
S1 30S Non-specific mRNA binding
S4 30S Functional mutations (streptomycin)
S5 30S Functional mutations (streptomycin)
S7 30S mRNA and tRNA binding at the E site
S9 30S Interaction with P site tRNA
S11 30S mRNA and tRNA binding at the E site
S12 30S tRNA decoding at the A site
S13 30S Interaction with P site tRNA
L2 50S Required for peptidyl transferase
L3 50S Required for peptidyl transferase
L4 50S Lines peptide exit tunnel
L5 50S Interaction with P site tRNA
L10 (L7 ⁄ L12)
2
50S Factor-binding stalk
L11 50S Factor binding
L16 (L10e) 50S A site tRNA binding
L22 50S Lines peptide tunnel
L23 50S At tunnel exit, interacts with
chaperones and SRP
L24 50S At tunnel exit, interacts with
chaperones and SRP
Archaea and eukaryotes
L44e 50S Interacts with E site tRNA

Eukaryotes only
RACK1 40S Signalling, scaffold protein
D. E. Brodersen and P. Nissen The social life of ribosomal proteins
FEBS Journal 272 (2005) 2098–2108 ª 2005 FEBS 2101
surface during translation. Even though no crystal
structure has yet been determined for S1 (the protein
was absent from the crystals of the small ribosomal
subunit [30,31]), it appears likely from sequence con-
siderations that each domain folds as a five-stranded
b-barrel similar to the OB-fold proteins. Such domains
are commonly seen in proteins that bind RNA nonspe-
cifically and would allow S1 to tether a long stretch of
mRNA to the ribosome using its consecutive domains.
In fact, when comparing with similar proteins for
which the structure is known, such as the S1-like
domain from polynucleotide phosphorylase (PNPase
[32]) and other homologues, it appears that there
are conserved amino acids on one face of the protein
that would allow for the nonspecific binding of single-
stranded nucleotides [11].
However, the most important specific recognition of
mRNA, at least in bacteria, works by pairing of the
well-known Shine–Dalgarno sequence just upstream of
the translation initiation codon with the ‘anti-Shine–
Dalgarno’ sequence, a stretch of complementary poly-
nucleotides located in the 3¢ end of ribosomal 16S
rRNA [33]. It thus appears that even though the S1
protein may be responsible for high affinity binding of
mRNA to the ribosome, the ribosomal RNA still plays
an important role in this process.

Whereas bacterial ribosomes seem well-tuned to
translate mRNA as soon as it emerges from the tran-
scriptional machinery, the association of mRNA with
the eukaryotic ribosome is under complex regulation.
Numerous RNA-binding proteins cover the mRNA as
it is packaged and exported from the nucleus as a
heteronuclear ribonucleoparticle (hnRNP) complex.
These proteins are targeted by signalling pathways that
link to the initiation machinery. A key player in this
process is the receptor of activated C kinase (RACK1).
This protein was recently shown to be in fact a ribo-
somal protein [34], and localized as a seven-bladed
b-propeller structure near the mRNA exit site on the
40S subunit [35]. RACK1 is a typical scaffold protein
and it binds kinases such as protein kinase C (which
has been shown to activate translation) and the Src
kinase as well as mRNA-binding proteins such as
Scp160p (reviewed in [36]). These together suggest that
RACK1 orchestrates specific mRNA binding and acti-
vation of protein synthesis directly on the ribosome.
Interestingly, RACK1 also interacts with integrin b
and other receptors, and it may further serve as a plat-
form to recruit ribosomes for local translation of speci-
fic mRNAs, for example in focal adhesions [36].
In eukaryotes, a bypass of the canonical factor-based
initiation mechanism is possible, whereby secondary
structures on the mRNA can play a major role in
guiding the ribosome to internal ribosome entry sites
(IRES). The mechanism is exploited by many viruses
for efficient expression of viral genes, but is also used

A
B
C
RACK1
D
rpL11 (L5)
L1
S7
S11
rpS5 (S7)
rpS0
S1
Fig. 3. mRNA binding to the ribosome. (A)
A back view of the Thermus thermophilus
30S subunit showing (with purple spheres)
the location of mRNA as deduced by X-ray
crystallography [28]. Proteins that are known
to interact with the mRNA are shown in col-
our as in Fig. 1. Figure prepared with
PYMOL
[68]. (B) A cryoelectron microscopy recon-
struction of the Hepatitis C virus IRES
bound to the human 40S subunit (back view
of the subunit with the IRES in dark purple).
Reprinted with permission from [37]. Copy-
right 2001 AAAS. (C) The cryoelectron micro-
scopy structure of the cricket paralysis virus
IRES bound to the human 80S ribosome.
The figure shows a back view of the 40S
subunit with the IRES in light purple. (D)

Top view of the entire 80S ribosome of the
same structure as in C. Figure panels C and
D are reproduced from [38] with permission
from Elsevier.
The social life of ribosomal proteins D. E. Brodersen and P. Nissen
2102 FEBS Journal 272 (2005) 2098–2108 ª 2005 FEBS
by a substantial number of endogenous genes in the
cell. Cryoelectron microscopy studies have revealed the
impressive ingenuity with which these RNA elements
bind to the human 40S subunit (Fig. 3B,C) [37,38]. Of
these, the structure of the human 80S in complex with a
cricket paralysis virus IRES element shows that the
ribosomal proteins rpL1 (L10A, prokaryotic L1),
rpL11 (prokaryotic L5) and rpS5 (prokaryotic S7) all
contact the IRES element (Fig. 3D) [38]. With the iden-
tification and localization of RACK1 on the ribosome
it appears that this protein may also be involved in
IRES recognition [35]. Upon 40S IRES complex forma-
tion, RACK1 is pushed downwards and forms a con-
tact to the rear of the mRNA platform of the 40S
subunit, to the region ascribed to the rpS0 protein. The
conformational change and interactions, centred on
ribosomal proteins, are also of potential importance for
the canonical initiation mechanism, which will operate
from the same side on the ribosome. In particular, the
RACK1-mediated conformational change in the 40S
subunit may play a central role during initiation.
tRNA recognition and decoding
The ribosome contains three binding sites for tRNA,
termed the A, P and E sites (Fig. 1). Of these, the

A site (where the aminoacyl tRNA initially binds and is
selected) and the P site (where the peptidyl tRNA is
bound) are essential while the functional involvement
of the E (exit) site remains a debated issue [39]. From
the subunit crystal structures it can be seen that the cru-
cial operations in both the A and P sites are mainly
catalysed by the rRNA component of the ribosome.
Selection of cognate tRNA at the A site is thus carried
out by two universally conserved adenines (A1492 and
A1493 in Escherichia coli 16S) that presumably are
stacked in the interior of the penultimate helix 44 of
16S rRNA in the absence of tRNA [25,40].
Upon cognate tRNA interaction with the base trip-
let on mRNA in the A site, the two adenines have
been shown to flip out from their position inside helix
44 to make strong hydrogen bonds with the first two
bases of the duplex formed between tRNA and mRNA
[25]. This movement leads to small but concerted rear-
rangements throughout the 16S rRNA which presuma-
bly then trigger GTP hydrolysis on elongation factor
Tu (EF-Tu), which in turn signals that the tRNA has
been accepted [26]. Along with the tight interactions
with the cognate ternary complex a kinked conforma-
tion of the tRNA anticodon stem arises which then
presumably relaxes as a spring after GTPase-mediated
release of EF-Tu, thereby promoting the A site accom-
modation process [41]. Further structural work has
concluded that only upon cognate tRNA–mRNA
interaction can the energy barrier associated with the
transition of the adenines be overcome. The mechan-

ism thus provides a strong discrimination against near-
cognate tRNAs that have only a single mismatched
base pair and hence cannot be reliably rejected on the
basis of free energy only [26]. Ribosomal proteins are
not involved in this process except for a hydrogen
bond between a serine in S12 and one of the adenines
in position two. However, at the third (or ‘wobble’)
position, protein S12 in the small subunit plays a more
prominent role in the recognition process, in that it
coordinates a magnesium ion that lies at the interface
between crucial bases involved in decoding. However,
as the wobble position is much less strictly monitored
by the ribosome than the first two positions, the real
importance of S12 in decoding can be questioned.
Again it seems that the RNA has maintained the most
important role in the process.
The P site, where the peptidyl transfer reaction takes
place on the 50S, is also mostly composed of RNA.
However, two long C-terminal tails of small ribosomal
subunit proteins S9 and S13 that are otherwise located
at the top of the 30S, make their way down through
the head of the subunit and come very close to the
P site tRNA [40]. This might cause speculation as to a
possible functional role of the two proteins at the
P site, but this idea has recently been dismissed by
showing that mutant E. coli cells that have had the
C-termini of the two proteins removed are fully viable,
indicating that their ribosomes are active [42]. A slower
growth rate of these cells was observed, however, indi-
cating that the tails might play an architectural or weak

functional role. On the large subunit, no proteins make
direct contacts to the P site tRNA, yet the L5 protein is
close by interacting with the 5S rRNA resides on top of
the subunit cleft on the central protuberance.
The E site on the 30S subunit is more dominated
by protein than any of the two other tRNA binding
sites (Fig. 1A). Two proteins, S7 and S11, are both
believed to be in contact with E site tRNA, and S7
in particular contains a long hairpin structure that
might have a functional role in dislodging the tRNA
from the ribosome [40]. Furthermore, the L44e pro-
tein (corresponding to the L33 protein in eubacteria
[43]) interacts directly with the 3¢ CCA end of E site
tRNA [44].
Binding site for GTP-containing translation
factors
The S4, L6, L14 and L11 proteins and the stalk pro-
teins L10 and L7 ⁄ L12 form the factor-binding site at
D. E. Brodersen and P. Nissen The social life of ribosomal proteins
FEBS Journal 272 (2005) 2098–2108 ª 2005 FEBS 2103
the edge of the intersubunit cleft of the ribosome,
together with the sarcin-ricin loop and the L11 RNA
region (the GTPase-associated center, GAC) (Fig. 1B).
These components make direct contacts to, for exam-
ple, elongation factor EF-G and the aminoacyl tRNA–
EF-Tu ternary complex on the ribosome [41,45,46].
Concerted movements of these contact points relate to
decoding events on the small subunit, and associate
with conformational changes in factor complexes as
seen for aminoacyl tRNA–EF-Tu [41]. It remains

unclear how the GTPase activity of the GTP ⁄ GDP
binding translation factors is in fact activated, but the
the sarcin–ricin loop is the only ribosomal component
that comes close to the GTP cofactor in EF-G and
EF-Tu bound ribosome complexes. Thus, rRNA again
seems to be responsible for a central ribosomal activ-
ity, and proteins that have been suggested to activate
GTP hydrolysis, in particular L11 and L7 ⁄ L12, must
be now ruled out as having a direct role.
The peptidyl transferase and peptide exit tunnel
The heart of the ribosome, the peptidyl transferase
center, is devoid of protein residues, as mentioned in
the introduction. The L16 protein (L10e in eukaryo-
tes) comes the closest, yet it merely supports the
accommodation of aminoacyl tRNA in the A site
(Fig. 1B). Further down the polypeptide exit tunnel,
proteins L4 and L22 expose loops to the interior
tunnel surface and form a narrow constriction [23].
This site may serve as a sensory site, which could
monitor the functional state of the ribosome or per-
haps also signal sequences for specific targeting of
the polypeptide. It remains to be shown whether the
L4–L22 constriction has any such function. Point
mutations or even deletions in those regions of the
L4 and L22 proteins confer resistance to antibiotics
such as erythromycin, which otherwise block the tun-
nel and thereby inhibit protein synthesis [47,48].
Parts of L22 and L39e also line the tunnel, and are
part of what gives the tunnel its ‘Teflon-like’ proper-
ties [23].

Signal recognition, secretion and
chaperones
The tunnel exit area is a highly important platform for
external factors that interact with the nascent
chain, such as the signal recognition particle (SRP),
the membrane-embedded Sec61 and SecYEG com-
plexes of eukaryotes and prokaryotes, respectively, as
well as the trigger factor chaperone. The exit area is
encircled by several ribosomal proteins, including the
universally conserved L22, L23, L24 and L29 proteins
(Fig. 4). The L23 protein is the central anchoring point
for the SRP [49] and the trigger factor [50]. The ring
of proteins around the exit area also forms the interac-
tion site for the doughnut-shaped Sec61 complex
embedded in the endoplasmic reticulum membrane of
eukaryotic cells [51]. However, a tight seal is not
formed. Instead, the interaction is centred on specific
interaction points, again with L23 as a key player,
together with L19e, L24 and L29 [51].
Ribosomal proteins involved in nuclear export
It has been known for a long time that the nuclear
export of the 5S rRNA in eukaryotes depends on a
complex formation with the L5 protein and the tran-
scription factor TFIIIA [52]. L5 contains the nuclear
export signal, which is found in a leucine-rich region
in the middle of the protein [53]. Similarly, the yeast
ribosomal protein rpS15 is required for nuclear exit of
the 40S subunit [54]. A more sophisticated role is
played by the 60S L10e protein, which serves as the
binding site for the NMD3 protein – a nuclear export

factor of the entire 60S subunit [55,56]. In the cyto-
plasm, NMD3 bound to L10e is released again from
the 60S subunit by interaction with the cytoplasmic
GTPase Lsg1p [57].
Fig. 4. The exit of the peptide tunnel on the 50S subunit. A view
down the peptide tunnel from its exit at the back of the 50S
towards the peptidyl transferase site inside it. The 23S rRNA is
shown as a combined sticks and ribbon model and relevant pro-
teins on the subunit coloured in surface representation. Figure pre-
pared with
PYMOL [68].
The social life of ribosomal proteins D. E. Brodersen and P. Nissen
2104 FEBS Journal 272 (2005) 2098–2108 ª 2005 FEBS
Ribosomal proteins working off the ribosome
Several ribosomal proteins are known to be very
loosely attached to the ribosome and thus only spend
part of their time working in translation. As men-
tioned above, small ribosomal subunit S1 is loosely
attached to the 30S subunit, probably by two out of
the six repeated domains, and purified subunits are
always substoichiometric in this protein [31]. Some
ribosomal proteins have biological roles outside their
contribution to translation, such as S10, which was
shown early on to work as an antiterminator of tran-
scription of k phage N protein in E. coli [58]. Fur-
thermore, several ribosomal proteins are known to
regulate the expression of themselves or other ribosom-
al proteins through translational feedback, such as L4
that regulates S10 expression [59], and S8 that regu-
lates expression of L5 [60]. RNA sequence analysis

revealed that this regulation is based on a similarity
between the secondary structures of the ribosomal pro-
tein mRNAs and the corresponding rRNA structures
[61]. The RNA-binding abilities of ribosomal proteins
are thus being exploited to regulate ribosome turnover
in the cell.
The human RACK1 protein has also been linked
with a wealth of soluble proteins and membrane re-
ceptors (recently reviewed in [36]). It is possible that
some of these interactions involve RACK1 as a sol-
uble factor. It has been reported that a pool of free
RACK1 is formed by upregulation of the expression
level during stationary growth of Saccharomyces cere-
visiae [62], however, a later study indicates that there
is no significant pool of yeast RACK1 outside the
ribosome [63].
Ribosome assembly
Assembly of the dozens of components making up
each ribosomal subunit is an extremely delicate pro-
cess, of which we still understand little. What has been
established, however, is that ribosomal assembly is a
sequential rather than a concerted operation, requiring
that some proteins bind to the rRNA later than others.
Early in vitro reconstitution experiments with both the
small and large subunit established many of the inter-
dependencies of the individual ribosomal proteins dur-
ing assembly and showed that in each subunit some
proteins functioned as ‘initiators’ of assembly by being
able to bind directly to the naked rRNA [64,65]. While
the complete subunit structures enable us to confirm

many of these dependencies, they still fall short of
explaining the details of assembly, mainly because in
each case we only know the structural endpoint of
the process, namely the fully folded subunits. How-
ever, there are a few interesting aspects of assembly
that the structures have shed light on.
In their paper describing the details of protein–RNA
interactions in the 50S subunit, Klein et al. argue that
proteins joining the growing complex early during
assembly (‘early proteins’) must be those with the lar-
gest areas of interaction with rRNA [9]. This seems
intuitively right and the authors argue further that it
must be true because a strong binding power is needed
simply to overcome the energetic and entropic barriers
associated with the initial assembly. Their hypothesis
can be tested by calculating the areas of interaction for
each ribosomal protein based on the crystal structures.
In the 30S, for example, the six initiator proteins (S4,
S7, S8, S15, S17 and S20) representing roughly 6 ⁄ 21
(29%) of the total number of protein residues (assu-
ming roughly equal size) contribute approximately
35% of the total protein–RNA interface area. Thus
there seems to be a slightly larger relative protein–
RNA interface for early proteins; however, the way
this calculation is carried out can be debated.
One interesting aspect of the assembly process is how
the long extensions of some of the proteins are accom-
modated into the growing particle. Clearly, some con-
certed action is required if a tail extends far away from
a given protein, into another RNA domain, for exam-

ple. Klein et al. propose a hypothesis whereby the glob-
ular domain of these proteins first binds to a region of
rRNA with an intermediate structure similar to its final
conformation, thus stabilizing the protein on the RNA
before the tail (whether terminal or internal) is placed
in the structure [9]. Interestingly, the authors find that
extensions are present in four of six initiator proteins in
the 50S, whereas for the 30S particle all initiators are
globular proteins devoid of tails [10]. The only consen-
sus we can derive from this is that a globular domain
with strong RNA-binding abilities is probably import-
ant for initiators during early assembly.
Ribosomal assembly in prokaryotes must be seen in
the context of transcription of the ribosomal RNA, in
that the process probably begins as soon as the 5¢ end
of the nascent RNA protrudes from the polymerase
complex. Chemical probing of 30S assembly intermedi-
ates carried out in the Noller lab has shown that
assembly does indeed proceed in a 5¢)3¢ direction [66],
and this seems to correlate well with the observed
interactions of proteins and rRNA as a function of
each protein’s location in the reconstitution diagram
[10]. In other words, ‘early proteins’ are primarily
found to interact with the 5¢ end of rRNA and late
proteins likewise mainly have interactions near the 3¢
end. In the large subunit, Klein et al. note that pro-
D. E. Brodersen and P. Nissen The social life of ribosomal proteins
FEBS Journal 272 (2005) 2098–2108 ª 2005 FEBS 2105
teins with extensive areas of rRNA interaction (hence
assumed to be ‘early’) primarily bind to domain I, the

5¢ domain of 23S rRNA [9], consistent with the direc-
tionality assumption.
Conclusion
Ribosomal proteins remain at the periphery of transla-
tion in more than one sense. First and foremost, they
are (with a few noteworthy exceptions) located on
the surface of the particle and therefore generally
far from the ‘real action’ at the centre. Second, most
biochemical and structural evidence now all but
exclude the proteins from the inner circle of chemical
catalysts involved in the essential processes of transla-
tion, in particular peptidyl transfer. However, as we
hope to have illustrated above, ribosomal proteins are
still much more than merely ‘RNA glue’ that hold the
ribosomal RNA in place – they do have a real social
life!
Being at the surface of the particle, the proteins are
in the best possible position to mediate the many inter-
actions of the ribosome, particularly in higher organ-
isms where the level of organization is so much
greater. This is perhaps also visible by the mere fact
that ribosomal proteins are larger and more plentiful
in the eukaryotes. The field of ribosome research has
for several decades been looking at the particle as
an isolated protein-synthesizing machine, probably
because its sheer size seemed daunting enough. But
recent research has begun to expand this horizon, and
thus try to understand the ribosome in a larger, cellu-
lar context. This has been elegantly demonstrated by
the cryoelectron microscopy structures of the yeast

ribosome bound to its protein-conducting channel on
the endoplasmic reticulum [51] and the recent identifi-
cation of RACK1, a scaffold protein involved in signal
transduction, as a ribosomal protein [35]. Common to
many of these ‘extraterrestrial’ activities of the ribo-
some is the strong involvement of ribosomal proteins
and we envisage that many new such connections will
be discovered in the future. It therefore may well be
that the ribosomal proteins, in fact, are the social life
of the ribosome.
Acknowledgements
We appreciate useful discussions with V. Ramakrish-
nan, T. A. Steitz, and P. B. Moore on matters
presented in this review. We are furthermore grateful
to Jakob Nilsson for valuable comments and sugges-
tions and Joachim Frank for providing the cryo-EM
figures in Fig. 3.
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