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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
2awb
Jmol
Contents
Protein chains
94 a.a. *
267 a.a. *
209 a.a. *
201 a.a. *
178 a.a. *
176 a.a. *
149 a.a. *
140 a.a. *
121 a.a. *
144 a.a. *
136 a.a. *
127 a.a. *
117 a.a. *
114 a.a. *
117 a.a. *
103 a.a. *
110 a.a. *
99 a.a. *
102 a.a. *
84 a.a. *
63 a.a. *
58 a.a. *
70 a.a. *
56 a.a. *
54 a.a. *
46 a.a. *
64 a.a. *
38 a.a. *
141 a.a. *
DNA/RNA
Metals
_MG ×111
Waters ×512
* Residue conservation analysis
PDB id:
2awb
Name: Ribosome
Title: Crystal structure of the bacterial ribosome from escherichia coli at 3.5 a resolution. This file contains the 50s subunit of the second 70s ribosome. The entire crystal structure contains two 70s ribosomes and is described in remark 400.
Structure: 5s ribosomal RNA. Chain: a. 23s ribosomal RNA. Chain: b. 50s ribosomal protein l25. Chain: v. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3.
Source: Escherichia coli. Organism_taxid: 562. Strain: mre600. Strain: mre600
Biol. unit: 31mer (from PQS)
Resolution:
3.46Å     R-factor:   0.279     R-free:   0.331
Authors: B.S.Schuwirth,M.A.Borovinskaya,C.W.Hau,W.Zhang,A.Vila- Sanjurjo,J.M.Holton,J.H.D.Cate
Key ref:
B.S.Schuwirth et al. (2005). Structures of the bacterial ribosome at 3.5 A resolution. Science, 310, 827-834. PubMed id: 16272117 DOI: 10.1126/science.1117230
Date:
31-Aug-05     Release date:   08-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc: 		94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2
Seq:
Struc: 		273 a.a.
267 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3
Seq:
Struc: 		209 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
P60723  (RL4_ECOLI) -  50S ribosomal protein L4
Seq:
Struc: 		201 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
P62399  (RL5_ECOLI) -  50S ribosomal protein L5
Seq:
Struc: 		179 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6
Seq:
Struc: 		177 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9
Seq:
Struc: 		149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13
Seq:
Struc: 		142 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14
Seq:
Struc: 		123 a.a.
121 a.a.
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15
Seq:
Struc: 		144 a.a.
144 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY7  (RL16_ECOLI) -  50S ribosomal protein L16
Seq:
Struc: 		136 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17
Seq:
Struc: 		127 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18
Seq:
Struc: 		117 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19
Seq:
Struc: 		115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20
Seq:
Struc: 		118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG48  (RL21_ECOLI) -  50S ribosomal protein L21
Seq:
Struc: 		103 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
P61175  (RL22_ECOLI) -  50S ribosomal protein L22
Seq:
Struc: 		110 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23
Seq:
Struc: 		100 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24
Seq:
Struc: 		104 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27
Seq:
Struc: 		85 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29
Seq:
Struc: 		63 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG51  (RL30_ECOLI) -  50S ribosomal protein L30
Seq:
Struc: 		59 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M9  (RL31_ECOLI) -  50S ribosomal protein L31
Seq:
Struc: 		70 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33
Seq:
Struc: 		55 a.a.
54 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P5  (RL34_ECOLI) -  50S ribosomal protein L34
Seq:
Struc: 		46 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q1  (RL35_ECOLI) -  50S ribosomal protein L35
Seq:
Struc: 		65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q6  (RL36_ECOLI) -  50S ribosomal protein L36
Seq:
Struc: 		38 a.a.
38 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11
Seq:
Struc: 		142 a.a.
141 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     response to antibiotic   9 terms 
  Biochemical function     structural constituent of ribosome     12 terms  

 

 
DOI no: 10.1126/science.1117230 Science 310:827-834 (2005)
PubMed id: 16272117  
 
 
Structures of the bacterial ribosome at 3.5 A resolution.
B.S.Schuwirth, M.A.Borovinskaya, C.W.Hau, W.Zhang, A.Vila-Sanjurjo, J.M.Holton, J.H.Cate.
 
  ABSTRACT  
 
We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.
 
  Selected figure(s)  
 
Figure 6.
Fig. 6. Molecular interactions in the intersubunit bridges. (A) Contact between S13 and L5 in ribosome I. (B) Contact between S13 and L5 in ribosome II. Only the C traces for the proteins are shown, because protein side chains are not clear in the electron density of either ribosome. Residues that become inaccessible to solvent (44) are indicated in orange for L5 and in yellow for S13 and S19. The direction of view is indicated in the center. (C) Molecular interactions in bridge B3. (D) Molecular interactions in bridge B7a. (E) Molecular interactions in bridge B6. Waters modeled at the interface are shown as red spheres inside the water-accessible volume, green mesh. (F) Close approach of phosphates at the subunit interface near bridge B2c. Distances (in angstroms) between phosphate oxygens are marked. 		Figure 7.
Fig. 7. Intersubunit bridges B2a and B4. (A) Minor-groove interactions between H69 and h44 and h45, broken down by region. Atoms within hydrogen-bonding distance, as mentioned in the text, are connected by dashed lines. (B) Molecular interactions in bridge B4. Protein S15 in the 30S subunit is in blue, with relevant side chains in green. The interaction is viewed from the left side of Fig. 5A (left) and from the right side of Fig. 5A (right). Electron density is visible for the side chain of Arg88 (R88) in ribosome II, but not in ribosome I. Other amino acid abbreviations: I, Ile; L, Leu; V, Val; A, Ala; Q, Gln.
 
  The above figures are reprinted by permission from the AAAs: Science (2005, 310, 827-834) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21256733 A.Petrov, G.Kornberg, S.O'Leary, A.Tsai, S.Uemura, and J.D.Puglisi (2011).
Dynamics of the translational machinery.
  Curr Opin Struct Biol, 21, 137-145.  
21368145 A.S.Yassin, M.E.Haque, P.P.Datta, K.Elmore, N.K.Banavali, L.L.Spremulli, and R.K.Agrawal (2011).
Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1.
  Proc Natl Acad Sci U S A, 108, 3918-3923.
PDB codes: 3izy 3izz
20969605 A.Vendeville, D.Larivière, and E.Fourmentin (2011).
An inventory of the bacterial macromolecular components and their spatial organization.
  FEMS Microbiol Rev, 35, 395-414.  
21549313 C.Chen, B.Stevens, J.Kaur, D.Cabral, H.Liu, Y.Wang, H.Zhang, G.Rosenblum, Z.Smilansky, Y.E.Goldman, and B.S.Cooperman (2011).
Single-molecule fluorescence measurements of ribosomal translocation dynamics.
  Mol Cell, 42, 367-377.  
20876687 C.Geary, A.Chworos, and L.Jaeger (2011).
Promoting RNA helical stacking via A-minor junctions.
  Nucleic Acids Res, 39, 1066-1080.  
21292166 D.Huber, N.Rajagopalan, S.Preissler, M.A.Rocco, F.Merz, G.Kramer, and B.Bukau (2011).
SecA interacts with ribosomes in order to facilitate posttranslational translocation in bacteria.
  Mol Cell, 41, 343-353.  
21399643 D.N.Ermolenko, and H.F.Noller (2011).
mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
  Nat Struct Mol Biol, 18, 457-462.  
21316217 D.N.Wilson, and R.Beckmann (2011).
The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling.
  Curr Opin Struct Biol, 21, 274-282.  
21370971 D.V.Fedyukina, and S.Cavagnero (2011).
Protein folding at the exit tunnel.
  Annu Rev Biophys, 40, 337-359.  
21410646 F.J.Blanco, and G.Montoya (2011).
Transient DNA / RNA-protein interactions.
  FEBS J, 278, 1643-1650.  
21292164 H.Ramu, N.Vázquez-Laslop, D.Klepacki, Q.Dai, J.Piccirilli, R.Micura, and A.S.Mankin (2011).
Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center.
  Mol Cell, 41, 321-330.  
21383139 J.Fu, J.B.Munro, S.C.Blanchard, and J.Frank (2011).
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
  Proc Natl Acad Sci U S A, 108, 4817-4821.  
21281690 K.Kipper, S.Sild, C.Hetényi, J.Remme, and A.Liiv (2011).
Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1.
  Biochimie, 93, 834-844.  
21151118 L.F.Estrozi, D.Boehringer, S.O.Shan, N.Ban, and C.Schaffitzel (2011).
Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor.
  Nat Struct Mol Biol, 18, 88-90.  
21342782 L.R.Cruz-Vera, M.S.Sachs, C.L.Squires, and C.Yanofsky (2011).
Nascent polypeptide sequences that influence ribosome function.
  Curr Opin Microbiol, 14, 160-166.  
21428957 M.V.Rodnina, and W.Wintermeyer (2011).
The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation.
  Biochem Soc Trans, 39, 658-662.  
21138965 Q.Sun, A.Vila-Sanjurjo, and M.O'Connor (2011).
Mutations in the intersubunit bridge regions of 16S rRNA affect decoding and subunit-subunit interactions on the 70S ribosome.
  Nucleic Acids Res, 39, 3321-3330.  
21267063 S.Bhushan, T.Hoffmann, B.Seidelt, J.Frauenfeld, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2011).
SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center.
  PLoS Biol, 9, e1000581.  
21217697 S.Feng, H.Li, J.Zhao, K.Pervushin, K.Lowenhaupt, T.U.Schwartz, and P.Dröge (2011).
Alternate rRNA secondary structures as regulators of translation.
  Nat Struct Mol Biol, 18, 169-176.
PDB code: 2l54
21415317 T.L.Grove, J.S.Benner, M.I.Radle, J.H.Ahlum, B.J.Landgraf, C.Krebs, and S.J.Booker (2011).
A radically different mechanism for S-adenosylmethionine-dependent methyltransferases.
  Science, 332, 604-607.  
21365677 W.Li, L.G.Trabuco, K.Schulten, and J.Frank (2011).
Molecular dynamics of EF-G during translocation.
  Proteins, 79, 1478-1486.
PDB code: 3izp
21368154 Z.Guo, M.Gibson, S.Sitha, S.Chu, and U.Mohanty (2011).
Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome.
  Proc Natl Acad Sci U S A, 108, 3947-3951.  
21109664 A.Ben-Shem, L.Jenner, G.Yusupova, and M.Yusupov (2010).
Crystal structure of the eukaryotic ribosome.
  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
20207951 A.E.Bunner, A.H.Beck, and J.R.Williamson (2010).
Kinetic cooperativity in Escherichia coli 30S ribosomal subunit reconstitution reveals additional complexity in the assembly landscape.
  Proc Natl Acad Sci U S A, 107, 5417-5422.  
20188109 A.E.Bunner, S.Nord, P.M.Wikström, and J.R.Williamson (2010).
The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution.
  J Mol Biol, 398, 1-7.  
20110260 A.E.Scheunemann, W.D.Graham, F.A.Vendeix, and P.F.Agris (2010).
Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA.
  Nucleic Acids Res, 38, 3094-3105.  
20855725 B.Llano-Sotelo, J.Dunkle, D.Klepacki, W.Zhang, P.Fernandes, J.H.Cate, and A.S.Mankin (2010).
Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.
  Antimicrob Agents Chemother, 54, 4961-4970.
PDB codes: 1vt2 3or9 3ora 3orb
20176963 B.Roy-Chaudhuri, N.Kirthi, and G.M.Culver (2010).
Appropriate maturation and folding of 16S rRNA during 30S subunit biogenesis are critical for translational fidelity.
  Proc Natl Acad Sci U S A, 107, 4567-4572.  
20541504 B.Sander, M.M.Golas, R.Lührmann, and H.Stark (2010).
An approach for de novo structure determination of dynamic molecular assemblies by electron cryomicroscopy.
  Structure, 18, 667-676.  
20192783 C.E.Aitken, A.Petrov, and J.D.Puglisi (2010).
Single ribosome dynamics and the mechanism of translation.
  Annu Rev Biophys, 39, 491-513.  
20562856 C.E.Aitken, and J.D.Puglisi (2010).
Following the intersubunit conformation of the ribosome during translation in real time.
  Nat Struct Mol Biol, 17, 793-800.  
20236470 E.Westhof (2010).
The amazing world of bacterial structured RNAs.
  Genome Biol, 11, 108.  
20797628 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.  
20403329 G.Cannarozzi, G.Cannarrozzi, N.N.Schraudolph, M.Faty, P.von Rohr, M.T.Friberg, A.C.Roth, P.Gonnet, G.Gonnet, and Y.Barral (2010).
A role for codon order in translation dynamics.
  Cell, 141, 355-367.  
20494981 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.  
20208344 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.  
20507916 I.Besseová, K.Réblová, N.B.Leontis, and J.Sponer (2010).
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.
  Nucleic Acids Res, 38, 6247-6264.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20876128 J.A.Dunkle, L.Xiong, A.S.Mankin, and J.H.Cate (2010).
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
  Proc Natl Acad Sci U S A, 107, 17152-17157.
PDB codes: 3oaq 3oar 3oas 3oat 3ofa 3ofb 3ofc 3ofd 3ofo 3ofp 3ofq 3ofr 3ofx 3ofy 3ofz 3og0
21057527 J.B.Munro, M.R.Wasserman, R.B.Altman, L.Wang, and S.C.Blanchard (2010).
Correlated conformational events in EF-G and the ribosome regulate translocation.
  Nat Struct Mol Biol, 17, 1470-1477.  
20018653 J.B.Munro, R.B.Altman, C.S.Tung, J.H.Cate, K.Y.Sanbonmatsu, and S.C.Blanchard (2010).
Spontaneous formation of the unlocked state of the ribosome is a multistep process.
  Proc Natl Acad Sci U S A, 107, 709-714.  
20235828 J.Frank, and R.L.Gonzalez (2010).
Structure and dynamics of a processive Brownian motor: the tran