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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
2i2t
Jmol
Contents
Protein chains
271 a.a. *
209 a.a. *
201 a.a. *
178 a.a. *
176 a.a. *
149 a.a. *
141 a.a. *
142 a.a. *
121 a.a. *
143 a.a. *
136 a.a. *
120 a.a. *
116 a.a. *
114 a.a. *
117 a.a. *
103 a.a. *
110 a.a. *
93 a.a. *
102 a.a. *
94 a.a. *
79 a.a. *
77 a.a. *
63 a.a. *
58 a.a. *
56 a.a. *
50 a.a. *
46 a.a. *
64 a.a. *
38 a.a. *
DNA/RNA
Metals
_MG ×119
_ZN
Waters ×556
* Residue conservation analysis
PDB id:
2i2t
Name: Ribosome
Title: Crystal structure of ribosome with messenger RNA and the anticodon stem-loop of p-site tRNA. This file contains the 50s subunit of one 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 l2. Chain: c. 50s ribosomal protein l3. Chain: d. 50s ribosomal protein l4.
Source: Escherichia coli. Organism_taxid: 562. Strain: mre600. Strain: mre600
Biol. unit: 31mer (from PQS)
Resolution:
3.22Å     R-factor:   0.287     R-free:   0.320
Authors: V.Berk,W.Zhang,R.D.Pai,J.H.D.Cate
Key ref:
V.Berk et al. (2006). Structural basis for mRNA and tRNA positioning on the ribosome. Proc Natl Acad Sci U S A, 103, 15830-15834. PubMed id: 17038497 DOI: 10.1073/pnas.0607541103
Date:
16-Aug-06     Release date:   24-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2
Seq:
Struc: 		273 a.a.
271 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 ?
P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11
Seq:
Struc: 		142 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13
Seq:
Struc: 		142 a.a.
142 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.
143 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.
120 a.a.
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18
Seq:
Struc: 		117 a.a.
116 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.
93 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 ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc: 		94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27
Seq:
Struc: 		85 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M2  (RL28_ECOLI) -  50S ribosomal protein L28
Seq:
Struc: 		78 a.a.
77 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 ?
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.
50 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.
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     11 terms  

 

 
DOI no: 10.1073/pnas.0607541103 Proc Natl Acad Sci U S A 103:15830-15834 (2006)
PubMed id: 17038497  
 
 
Structural basis for mRNA and tRNA positioning on the ribosome.
V.Berk, W.Zhang, R.D.Pai, J.H.Cate, J.H.Cate.
 
  ABSTRACT  
 
Protein synthesis requires the accurate positioning of mRNA and tRNA in the peptidyl-tRNA site of the ribosome. Here we describe x-ray crystal structures of the intact bacterial ribosome from Escherichia coli in a complex with mRNA and the anticodon stem-loop of P-site tRNA. At 3.5-A resolution, these structures reveal rearrangements in the intact ribosome that clamp P-site tRNA and mRNA on the small ribosomal subunit. Binding of the anticodon stem-loop of P-site tRNA to the ribosome is sufficient to lock the head of the small ribosomal subunit in a single conformation, thereby preventing movement of mRNA and tRNA before mRNA decoding.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Interactions between the ribosome and mRNA in the P site. (A) Hydrogen bonds to the phosphates of nucleotides +1 and +3 of mRNA shown from the perspective of the 30S head. The position of G1401 and a fully hydrated Mg^2+ have been removed for clarity. (B) Coordination of a fully hydrated Mg^2+ to 16S rRNA and the backbone of mRNA, shown from the perspective of the subunit body. (C) View of (F[obs] – F[calc]) difference electron density in the electronegative pocket between the backbone of P-site mRNA and helix-44 nucleotides 1494–1498 in 16S rRNA. The position of A1493 is already adjusted to fit the electron density. (D) Nucleotides +4 through +6 of the mRNA, along with two Mg^2+ ions, modeled into the electron density in C followed by refinement. 		Figure 3.
Fig. 3. Ribosome interactions with the P-site ASL. (A) Closing of the P-site cleft when compared with the 30S ribosome structures (9). Changes in the distance between C1400 and G966 and between G966 and ASL are indicated by arrows and distances. The position of the very C terminus of protein S9 is indicated. The view is from the aminoacyl-tRNA site in the small subunit. (B) Stereoview of the averaged (3F[obs] – 2F[calc]) difference electron density for the 30S contacts to the ASL shown in A. Electron density for mRNA nucleotides +4 through +6 has been removed for clarity. The density indicated by an asterisk is disconnected from that for protein S9 and therefore has not been assigned. (C) Minor groove interactions among G1338, A1339, and the P-site ASL. The view is from the right in A, i.e., from the perspective of the 50S subunit.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21499241 J.Frauenfeld, J.Gumbart, E.O.Sluis, S.Funes, M.Gartmann, B.Beatrix, T.Mielke, O.Berninghausen, T.Becker, K.Schulten, and R.Beckmann (2011).
Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
  Nat Struct Mol Biol, 18, 614-621.
PDB codes: 3j00 3j01
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.  
21245352 J.Zhu, A.Korostelev, D.A.Costantino, J.P.Donohue, H.F.Noller, and J.S.Kieft (2011).
Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
  Proc Natl Acad Sci U S A, 108, 1839-1844.
PDB codes: 3pyn 3pyo 3pyq 3pyr 3pys 3pyt 3pyu 3pyv
21152561 K.Mikulík, J.Bobek, A.Ziková, M.Smětáková, and S.Bezoušková (2011).
Phosphorylation of ribosomal proteins influences subunit association and translation of poly (U) in Streptomyces coelicolor.
  Mol Biosyst, 7, 817-823.  
21378755 X.Agirrezabala, E.Schreiner, L.G.Trabuco, J.Lei, R.F.Ortiz-Meoz, K.Schulten, R.Green, and J.Frank (2011).
Structural insights into cognate versus near-cognate discrimination during decoding.
  EMBO J, 30, 1497-1507.
PDB codes: 3izt 3izu 3izv 3izw
20048003 A.K.Saini, J.S.Nanda, J.R.Lorsch, and A.G.Hinnebusch (2010).
Regulatory elements in eIF1A control the fidelity of start codon selection by modulating tRNA(i)(Met) binding to the ribosome.
  Genes Dev, 24, 97.  
20673207 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.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
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 translating ribosome.
  Annu Rev Biochem, 79, 381-412.  
20694005 L.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural rearrangements of the ribosome at the tRNA proofreading step.
  Nat Struct Mol Biol, 17, 1072-1078.  
19914248 P.Khade, and S.Joseph (2010).
Functional interactions by transfer RNAs in the ribosome.
  FEBS Lett, 584, 420-426.  
19965768 S.Kimura, and T.Suzuki (2010).
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.
  Nucleic Acids Res, 38, 1341-1352.  
19298824 A.Alian, A.DeGiovanni, S.L.Griner, J.S.Finer-Moore, and R.M.Stroud (2009).
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
  J Mol Biol, 388, 785-800.
PDB code: 3dh3
19095617 A.Devaraj, S.Shoji, E.D.Holbrook, and K.Fredrick (2009).
A role for the 30S subunit E site in maintenance of the translational reading frame.
  RNA, 15, 255-265.  
19279186 C.Hsiao, and L.D.Williams (2009).
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.
  Nucleic Acids Res, 37, 3134-3142.  
19628620 C.Hsiao, S.Mohan, B.K.Kalahar, and L.D.Williams (2009).
Peeling the onion: ribosomes are ancient molecular fossils.
  Mol Biol Evol, 26, 2415-2425.  
  19539793 C.U.Hellen (2009).
IRES-induced conformational changes in the ribosome and the mechanism of translation initiation by internal ribosomal entry.
  Biochim Biophys Acta, 1789, 558-570.  
19036786 D.Benelli, S.Marzi, C.Mancone, T.Alonzi, A.la Teana, and P.Londei (2009).
Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya.
  Nucleic Acids Res, 37, 256-267.  
20004163 D.J.Taylor, B.Devkota, A.D.Huang, M.Topf, E.Narayanan, A.Sali, S.C.Harvey, and J.Frank (2009).
Comprehensive molecular structure of the eukaryotic ribosome.
  Structure, 17, 1591-1604.
PDB codes: 3jyv 3jyw 3jyx
19190093 D.L.Bellur, and S.A.Woodson (2009).
A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly.
  Nucleic Acids Res, 37, 1886-1896.  
19154330 D.Qin, and K.Fredrick (2009).
Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA.
  Mol Microbiol, 71, 1239-1249.  
19122150 E.Villa, J.Sengupta, L.G.Trabuco, J.LeBarron, W.T.Baxter, T.R.Shaikh, R.A.Grassucci, P.Nissen, M.Ehrenberg, K.Schulten, and J.Frank (2009).
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.
  Proc Natl Acad Sci U S A, 106, 1063-1068.
PDB codes: 3fih 3fik
19469554 G.Y.Soung, J.L.Miller, H.Koc, and E.C.Koc (2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
  J Proteome Res, 8, 3390-3402.  
19647434 J.B.Munro, K.Y.Sanbonmatsu, C.M.Spahn, and S.C.Blanchard (2009).
Navigating the ribosome's metastable energy landscape.
  Trends Biochem Sci, 34, 390-400.  
19258537 J.F.Atkins, and G.R.Björk (2009).
A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment.
  Microbiol Mol Biol Rev, 73, 178-210.  
19913480 J.Gumbart, L.G.Trabuco, E.Schreiner, E.Villa, and K.Schulten (2009).
Regulation of the protein-conducting channel by a bound ribosome.
  Structure, 17, 1453-1464.
PDB codes: 3kc4 3kcr
19197244 M.Lovmar, K.Nilsson, E.Lukk, V.Vimberg, T.Tenson, and M.Ehrenberg (2009).
Erythromycin resistance by L4/L22 mutations and resistance masking by drug efflux pump deficiency.
  EMBO J, 28, 736-744.  
19417061 S.Shoji, N.M.Abdi, R.Bundschuh, and K.Fredrick (2009).
Contribution of ribosomal residues to P-site tRNA binding.
  Nucleic Acids Res, 37, 4033-4042.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
19561193 Y.Yu, A.Marintchev, V.G.Kolupaeva, A.Unbehaun, T.Veryasova, S.C.Lai, P.Hong, G.Wagner, C.U.Hellen, and T.V.Pestova (2009).
Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing.
  Nucleic Acids Res, 37, 5167-5182.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18157137 B.Kastner, N.Fischer, M.M.Golas, B.Sander, P.Dube, D.Boehringer, K.Hartmuth, J.Deckert, F.Hauer, E.Wolf, H.Uchtenhagen, H.Urlaub, F.Herzog, J.M.Peters, D.Poerschke, R.Lührmann, and H.Stark (2008).
GraFix: sample preparation for single-particle electron cryomicroscopy.
  Nat Methods, 5, 53-55.  
17981968 C.Wicker-Planquart, A.E.Foucher, M.Louwagie, R.A.Britton, and J.M.Jault (2008).
Interactions of an essential Bacillus subtilis GTPase, YsxC, with ribosomes.
  J Bacteriol, 190, 681-690.  
18157151 D.A.Costantino, J.S.Pfingsten, R.P.Rambo, and J.S.Kieft (2008).
tRNA-mRNA mimicry drives translation initiation from a viral IRES.
  Nat Struct Mol Biol, 15, 57-64.
PDB code: 3b31
18768810 E.Roberts, A.Sethi, J.Montoya, C.R.Woese, and Z.Luthey-Schulten (2008).
Molecular signatures of ribosomal evolution.
  Proc Natl Acad Sci U S A, 105, 13953-13958.  
18455733 G.Blaha, G.Gürel, S.J.Schroeder, P.B.Moore, and T.A.Steitz (2008).
Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
  J Mol Biol, 379, 505-519.
PDB codes: 3cc2 3cc4 3cc7 3cce 3ccj 3ccl 3ccm 3ccq 3ccr 3ccs 3ccu 3ccv 3cd6
18286627 J.B.Munro, A.Vaiana, K.Y.Sanbonmatsu, and S.C.Blanchard (2008).
A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.