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234 a.a.
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206 a.a.
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208 a.a.
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150 a.a.
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101 a.a.
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155 a.a.
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138 a.a.
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127 a.a.
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98 a.a.
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119 a.a.
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124 a.a.
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125 a.a.
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60 a.a.
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88 a.a.
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83 a.a.
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104 a.a.
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73 a.a.
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80 a.a.
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99 a.a.
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24 a.a.
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Obsolete entry |
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PDB id:
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| Name: |
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Ribosome
|
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Title:
|
|
Structure of the thermus thermophilus 30s ribosomal subunit
|
|
Structure:
|
|
16s ribosomal RNA. Chain: a. Fragment of messenger RNA. Chain: x. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4.
|
|
Source:
|
|
Thermus thermophilus. Bacteria. Bacteria
|
|
Biol. unit:
|
|
22mer (from
)
|
|
Resolution:
|
|
|
3.05Å
|
R-factor:
|
0.208
|
R-free:
|
0.252
|
|
|
Authors:
|
|
B.T.Wimberly,D.E.Brodersen,W.M.Clemons Jr.,R.Morgan-Warren, A.P.Carter,C.Vonrhein,T.Hartsch,V.Ramakrishnan
|
Key ref:
|
|
B.T.Wimberly
et al.
(2000).
Structure of the 30S ribosomal subunit.
Nature,
407,
327-339.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
08-Aug-00
|
Release date:
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25-Sep-00
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PROCHECK
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Headers
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References
|
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No UniProt id for this chain
|
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No UniProt id for this chain
|
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|
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|
|
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|
|
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P80373
(RS4_THET8) -
30S ribosomal protein S4 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
|
|
|
|
Seq:
Struc:
|
|
|
|
209 a.a.
208 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P27152
(RS5_THETH) -
30S ribosomal protein S5 from Thermus thermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
162 a.a.
150 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P23370
(RS6_THETH) -
30S ribosomal protein S6 from Thermus thermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
101 a.a.
101 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P17291
(RS7_THET8) -
30S ribosomal protein S7 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
|
|
|
|
Seq:
Struc:
|
|
|
|
156 a.a.
155 a.a.
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
P24319
(RS8_THETH) -
30S ribosomal protein S8 from Thermus thermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
138 a.a.
138 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P80375
(RS10_THETH) -
30S ribosomal protein S10 from Thermus thermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
105 a.a.
98 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
P17293
(RS12_THETH) -
30S ribosomal protein S12 from Thermus thermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
132 a.a.
124 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P24320
(RS14_THETH) -
30S ribosomal protein S14 type Z from Thermus thermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
61 a.a.
60 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P80378
(RS15_THETH) -
30S ribosomal protein S15 from Thermus thermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
89 a.a.
88 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P80381
(RS19_THETH) -
30S ribosomal protein S19 from Thermus thermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
93 a.a.
80 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Nature
407:327-339
(2000)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structure of the 30S ribosomal subunit.
|
|
B.T.Wimberly,
D.E.Brodersen,
W.M.Clemons,
R.J.Morgan-Warren,
A.P.Carter,
C.Vonrhein,
T.Hartsch,
V.Ramakrishnan.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Genetic information encoded in messenger RNA is translated into protein by the
ribosome, which is a large nucleoprotein complex comprising two subunits,
denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S
subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic
model rationalizes over four decades of biochemical data on the ribosome, and
provides a wealth of information about RNA and protein structure, protein-RNA
interactions and ribosome assembly. It is also a structural basis for analysis
of the functions of the 30S subunit, such as decoding, and for understanding the
action of antibiotics. The structure will facilitate the interpretation in
molecular terms of lower resolution structural data on several functional states
of the ribosome from electron microscopy and crystallography.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 4.
Figure 4: Structure of the 5' domain of 16S RNA. a, Stereo
view of the entire 5' domain, with an inset on the right showing
its location in the 30S subunit. The upper (b), middle (c) and
lower (d) subdomains are shown separately next to corresponding
parts of the secondary structure diagrams. The colours in the
secondary structure diagrams match those in the structure in
this and Figs 5 and 6.
|
|
Figure 6.
Figure 6: Structure of the 3' major and 3' minor domains of 16S
RNA. a, Stereo view of the 3' major domain with inset showing
its location in the 30S. b-d, The upper, middle and lower parts
of the 3' major domain, with corresponding secondary structure
diagrams. e, Stereo view of the 3' minor domain, with secondary
structure diagram and inset showing its location in the 30S.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2000,
407,
327-339)
copyright 2000.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
M.Selmer,
Y.G.Gao,
A.Weixlbaumer,
and
V.Ramakrishnan
(2012).
Ribosome engineering to promote new crystal forms.
|
| |
Acta Crystallogr D Biol Crystallogr,
68,
578-583.
|
|
|
|
|
|
|
S.Melnikov,
A.Ben-Shem,
N.Garreau de Loubresse,
L.Jenner,
G.Yusupova,
and
M.Yusupov
(2012).
One core, two shells: bacterial and eukaryotic ribosomes.
|
| |
Nat Struct Mol Biol,
19,
560-567.
|
|
|
|
|
|
|
C.W.Lee,
L.Li,
and
D.P.Giedroc
(2011).
The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold.
|
| |
FEBS Lett,
585,
1049-1053.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Rabl,
M.Leibundgut,
S.F.Ataide,
A.Haag,
and
N.Ban
(2011).
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
|
| |
Science,
331,
730-736.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Wang,
and
E.P.Nikonowicz
(2011).
Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA.
|
| |
J Mol Biol,
408,
99.
|
|
|
|
|
|
|
K.Fujii,
M.T.Young,
and
K.D.Harris
(2011).
Exploiting powder X-ray diffraction for direct structure determination in structural biology: The P2X4 receptor trafficking motif YEQGL.
|
| |
J Struct Biol,
174,
461-467.
|
|
|
|
|
|
|
M.Valle
(2011).
Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.
|
| |
Eur Biophys J,
40,
589-597.
|
|
|
|
|
|
|
Q.Xie,
J.Lin,
Y.Qin,
J.Zhou,
and
W.Bu
(2011).
Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.
|
| |
Protein Cell,
2,
161-170.
|
|
|
|
|
|
|
T.R.Blower,
X.Y.Pei,
F.L.Short,
P.C.Fineran,
D.P.Humphreys,
B.F.Luisi,
and
G.P.Salmond
(2011).
A processed noncoding RNA regulates an altruistic bacterial antiviral system.
|
| |
Nat Struct Mol Biol,
18,
185-190.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
V.N.Uversky
(2011).
Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes.
|
| |
Chem Soc Rev,
40,
1623-1634.
|
|
|
|
|
|
|
A.Ben-Shem,
L.Jenner,
G.Yusupova,
and
M.Yusupov
(2010).
Crystal structure of the eukaryotic ribosome.
|
| |
Science,
330,
1203-1209.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.H.Antonioli,
J.C.Cochrane,
S.V.Lipchock,
and
S.A.Strobel
(2010).
Plasticity of the RNA kink turn structural motif.
|
| |
RNA,
16,
762-768.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.M.Lopes,
R.N.Miguel,
C.A.Sargent,
P.J.Ellis,
A.Amorim,
and
N.A.Affara
(2010).
The human RPS4 paralogue on Yq11.223 encodes a structurally conserved ribosomal protein and is preferentially expressed during spermatogenesis.
|
| |
BMC Mol Biol,
11,
33.
|
|
|
|
|
|
|
A.Neueder,
S.Jakob,
G.Pöll,
J.Linnemann,
R.Deutzmann,
H.Tschochner,
and
P.Milkereit
(2010).
A local role for the small ribosomal subunit primary binder rpS5 in final 18S rRNA processing in yeast.
|
| |
PLoS One,
5,
e10194.
|
|
|
|
|
|
|
A.Ohman,
T.Oman,
and
M.Oliveberg
(2010).
Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P(54-55).
|
| |
Protein Sci,
19,
183-189.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.V.Surdina,
T.I.Rassokhin,
A.V.Golovin,
V.A.Spiridonova,
and
A.M.Kopylov
(2010).
Mapping the ribosomal protein S7 regulatory binding site on mRNA of the E. coli streptomycin operon.
|
| |
Biochemistry (Mosc),
75,
841-850.
|
|
|
|
|
|
|
B.M.Burmann,
X.Luo,
P.Rösch,
M.C.Wahl,
and
M.E.Gottesman
(2010).
Fine tuning of the E. coli NusB:NusE complex affinity to BoxA RNA is required for processive antitermination.
|
| |
Nucleic Acids Res,
38,
314-326.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.L.Ng,
K.Lang,
N.A.Meenan,
A.Sharma,
A.C.Kelley,
C.Kleanthous,
and
V.Ramakrishnan
(2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
|
| |
Nat Struct Mol Biol,
17,
1241-1246.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.Ackermann,
T.L.Schmidt,
J.S.Hannam,
C.S.Purohit,
A.Heckel,
and
M.Famulok
(2010).
A double-stranded DNA rotaxane.
|
| |
Nat Nanotechnol,
5,
436-442.
|
|
|
|
|
|
|
E.Capriotti,
and
M.A.Marti-Renom
(2010).
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.
|
| |
BMC Bioinformatics,
11,
322.
|
|
|
|
|
|
|
F.Brandt,
L.A.Carlson,
F.U.Hartl,
W.Baumeister,
and
K.Grünewald
(2010).
The three-dimensional organization of polyribosomes in intact human cells.
|
| |
Mol Cell,
39,
560-569.
|
|
|
|
|
|
|
F.J.Sun,
and
G.Caetano-Anollés
(2010).
The origin of modern 5S rRNA: a case of relating models of structural history to phylogenetic data.
|
| |
J Mol Evol,
71,
3-5.
|
|
|
|
|
|
|
G.Ciriello,
C.Gallina,
and
C.Guerra
(2010).
Analysis of interactions between ribosomal proteins and RNA structural motifs.
|
| |
BMC Bioinformatics,
11,
S41.
|
|
|
|
|
|
|
H.David-Eden,
A.S.Mankin,
and
Y.Mandel-Gutfreund
(2010).
Structural signatures of antibiotic binding sites on the ribosome.
|
| |
Nucleic Acids Res,
38,
5982-5994.
|
|
|
|
|
|
|
H.Demirci,
L.H.Larsen,
T.Hansen,
A.Rasmussen,
A.Cadambi,
S.T.Gregory,
F.Kirpekar,
and
G.Jogl
(2010).
Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.
|
| |
RNA,
16,
1584-1596.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Nanamiya,
and
F.Kawamura
(2010).
Towards an elucidation of the roles of the ribosome during different growth phases in Bacillus subtilis.
|
| |
Biosci Biotechnol Biochem,
74,
451-461.
|
|
|
|
|
|
|
H.S.Zaher,
and
R.Green
(2010).
Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection.
|
| |
Mol Cell,
39,
110-120.
|
|
|
|
|
|
|
J.Crandall,
M.Rodriguez-Lopez,
M.Pfeiffer,
B.Mortensen,
and
A.Buskirk
(2010).
rRNA mutations that inhibit transfer-messenger RNA activity on stalled ribosomes.
|
| |
J Bacteriol,
192,
553-559.
|
|
|
|
|
|
|
J.Frank,
and
R.L.Gonzalez
(2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
|
| |
Annu Rev Biochem,
79,
381-412.
|
|
|
|
|
|
|
J.Frank
(2010).
The Ribosome Comes Alive.
|
| |
Isr J Chem,
50,
95-98.
|
|
|
|
|
|
|
J.L.Houghton,
K.D.Green,
W.Chen,
and
S.Garneau-Tsodikova
(2010).
The future of aminoglycosides: the end or renaissance?
|
| |
Chembiochem,
11,
880-902.
|
|
|
|
|
|
|
J.Ouellet,
S.Melcher,
A.Iqbal,
Y.Ding,
and
D.M.Lilley
(2010).
Structure of the three-way helical junction of the hepatitis C virus IRES element.
|
| |
RNA,
16,
1597-1609.
|
|
|
|
|
|
|
J.P.Armache,
A.Jarasch,
A.M.Anger,
E.Villa,
T.Becker,
S.Bhushan,
F.Jossinet,
M.Habeck,
G.Dindar,
S.Franckenberg,
V.Marquez,
T.Mielke,
M.Thomm,
O.Berninghausen,
B.Beatrix,
J.Söding,
E.Westhof,
D.N.Wilson,
and
R.Beckmann
(2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
|
| |
Proc Natl Acad Sci U S A,
107,
19754-19759.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.P.Armache,
A.Jarasch,
A.M.Anger,
E.Villa,
T.Becker,
S.Bhushan,
F.Jossinet,
M.Habeck,
G.Dindar,
S.Franckenberg,
V.Marquez,
T.Mielke,
M.Thomm,
O.Berninghausen,
B.Beatrix,
J.Söding,
E.Westhof,
D.N.Wilson,
and
R.Beckmann
(2010).
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
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| |
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PDB code:
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U.Nagaswamy,
X.Gao,
S.A.Martinis,
and
G.E.Fox
(2001).
NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop.
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Nucleic Acids Res,
29,
5129-5139.
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PDB code:
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V.Ramakrishnan,
and
P.B.Moore
(2001).
Atomic structures at last: the ribosome in 2000.
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| |
Curr Opin Struct Biol,
11,
144-154.
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W.Cruse,
P.Saludjian,
A.Neuman,
and
T.Prangé
(2001).
Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues.
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| |
Acta Crystallogr D Biol Crystallogr,
57,
1609-1613.
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PDB codes:
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W.Li,
and
D.W.Hoffman
(2001).
Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy.
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| |
Protein Sci,
10,
2426-2438.
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PDB code:
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Y.G.Kim,
S.Maas,
and
A.Rich
(2001).
Comparative mutational analysis of cis-acting RNA signals for translational frameshifting in HIV-1 and HTLV-2.
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| |
Nucleic Acids Res,
29,
1125-1131.
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Z.Li,
G.Stahl,
and
P.J.Farabaugh
(2001).
Programmed +1 frameshifting stimulated by complementarity between a downstream mRNA sequence and an error-correcting region of rRNA.
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| |
RNA,
7,
275-284.
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C.E.Schutt,
and
U.Lindberg
(2000).
Forthcoming topics
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| |
Anat Rec,
261,
216.
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N.W.Isaacs
(2000).
Where is the information in structural space?. Editorial overview.
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| |
Curr Opin Struct Biol,
10,
631-632.
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S.Chandra Sanyal,
and
A.Liljas
(2000).
The end of the beginning: structural studies of ribosomal proteins.
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| |
Curr Opin Struct Biol,
10,
633-636.
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S.Connell,
and
K.Nierhaus
(2000).
Translational termination not yet at its end.
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| |
Chembiochem,
1,
250-253.
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T.Zhou,
M.Daugherty,
N.V.Grishin,
A.L.Osterman,
and
H.Zhang
(2000).
Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily.
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| |
Structure,
8,
1247-1257.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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