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PDBsum entry 2wdg
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
2wdg

 

 

 

 

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Contents
Protein chains
235 a.a. *
207 a.a. *
208 a.a. *
151 a.a. *
101 a.a. *
155 a.a. *
138 a.a. *
127 a.a. *
99 a.a. *
119 a.a. *
125 a.a. *
125 a.a. *
60 a.a. *
88 a.a. *
84 a.a. *
100 a.a. *
70 a.a. *
79 a.a. *
99 a.a. *
25 a.a. *
DNA/RNA
Ligands
PAR
Metals
_MG ×741
_ZN ×3
* Residue conservation analysis
Obsolete entry
PDB id:
2wdg
Name: Ribosome
Title: Structure of the thermus thermophilus 70s ribosome in complex with mRNA, paromomycin, acylated a-site tRNA, deacylated p-site tRNA, and e-site tRNA. This file contains the 30s subunit a-,p-, and e-site trnas and paromomycin for molecule i.
Structure: 16s rrna. Chain: a. Other_details: chain a (16s RNA) has e.Coli numbering, based on a structural alignment with the corresponding e.Coli structure in 2avy.. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Escherichia coli. Organism_taxid: 83333. Strain: k12. Synthetic: yes. Strain: k12
Resolution:
3.30Å     R-factor:   0.223     R-free:   0.272
Authors: R.M.Voorhees,A.Weixlbaumer,D.Loakes,A.C.Kelley, V.Ramakrishnan
Key ref:
R.M.Voorhees et al. (2009). Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Biol, 16, 528-533. PubMed id: 19363482 DOI: 10.1038/nsmb.1577
Date:
24-Mar-09     Release date:   14-Apr-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		256 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		239 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		162 a.a.
151 a.a.
Protein chain
Q5SLP8  (RS6_THET8) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Q5SHQ2  (RS8_THET8) - 
Protein chain
Pfam   ArchSchema ?
P62669  (RS9_THET2) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		128 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		132 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		126 a.a.
125 a.a.
Protein chain
Q5SHQ1  (RS14Z_THET8) - 
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
84 a.a.
Protein chain
Q5SHP7  (RS17_THET8) - 
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		93 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		106 a.a.
99 a.a.
Protein chain
Q5SIH3  (RSHX_THET8) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		27 a.a.
25 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1504 bases
  C-G-C-G-G-G-G-U-G-G-A-G-C-A-G-C-C-U-G-G-U-A-G-C-U-C-G-U-C-G-G-G-C-U-C-A-U-A-A- 77 bases
  G-C-C-C-G-G-A-U-A-G-C-U-C-A-G-U-C-G-G-U-A-G-A-G-C-A-G-G-G-G-A-U-U-G-A-A-A-A-U- 76 bases
  A-A-A-A-U-G-U-U-C-A 10 bases
  G-C-C-C-G-G-A-U-A-G-C-U-C-A-G-U-C-G-G-U-A-G-A-G-C-A-G-G-G-G-A-U-U-G-A-A-A-A-U- 77 bases

 

 
DOI no: 10.1038/nsmb.1577 Nat Struct Biol 16:528-533 (2009)
PubMed id: 19363482  
 
 
Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.
R.M.Voorhees, A.Weixlbaumer, D.Loakes, A.C.Kelley, V.Ramakrishnan.
 
  ABSTRACT  
 
Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3' ends of tRNA ligands. Here we present structures, at 3.6-A and 3.5-A resolution respectively, of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl-transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer.
 
  Selected figure(s)  
 
Figure 1.
(a) Chemical diagram of the pre-peptidyl-transfer state of the ribosomal active site. In this structure, both the A- and P-site tRNAs contain an amide linkage between residue A76 and the phenylalanine amino acid. (b) Model of the ribosomal active site in the pre-peptidyl-transfer state, including representative 3F[o] – 2F[c] density for the A- and P-site tRNAs in green and purple, respectively. (c) Chemical diagram of the post-peptidyl-transfer state in which the A site contains an amide-linked Phe-tRNA^Phe and the P site contains tRNA^fMet. (d) Model of the post-peptidyl-transfer state within the peptidyl transferase center, including 3F[o] – 2F[c] density for the A- and P-site tRNAs in green and purple, respectively. 		Figure 3.
(a) Overview of protein L27 in relation to the A- and P-site tRNAs (in green and purple, respectively). The protein (dark blue) contains a globular domain and an N-terminal extension that localizes between the 3' ends of the ribosomal tRNAs. (b) Predicted interactions of protein L27 with the ribosomal substrates and 23S RNA (light blue). The modeled interactions were observed in both structures containing occupied A sites, though the post-peptidyl-transfer structure is displayed here as it contained moderately better electron density for L27. A representative 3F[o] – 2F[c] electron density map is displayed in blue. (c) Overview of protein L16 in relation to the ribosomal substrates. The protein is located adjacent to the elbow of the A-site tRNA. (d) Interactions between the conserved residues Arg51 and Arg56 of protein L16 (dark blue) with the backbone of the A-site tRNA (green). Representative 3F[o] – 2F[c] density, as determined in the pre-peptidyl-transfer structure, is displayed in green for the region of the A-site tRNA predicted to interact with L16.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 528-533) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082171 D.Caetano-Anollés, K.M.Kim, J.E.Mittenthal, and G.Caetano-Anollés (2011).
Proteome evolution and the metabolic origins of translation and cellular life.
  J Mol Evol, 72, 14-33.  
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.  
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.  
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.  
21151095 M.Y.Pavlov, A.Zorzet, D.I.Andersson, and M.Ehrenberg (2011).
Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits.
  EMBO J, 30, 289-301.  
20375101 A.Chirkova, M.D.Erlacher, N.Clementi, M.Zywicki, M.Aigner, and N.Polacek (2010).
The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center.
  Nucleic Acids Res, 38, 4844-4855.  
20588254 A.Korostelev, J.Zhu, H.Asahara, and H.F.Noller (2010).
Recognition of the amber UAG stop codon by release factor RF1.
  EMBO J, 29, 2577-2585.
PDB codes: 3mr8 3mrz 3ms0 3ms1
20660012 A.Meskauskas, and J.D.Dinman (2010).
A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site.
  Nucleic Acids Res, 38, 7800-7813.  
20806270 C.G.Kurland (2010).
The RNA dreamtime: modern cells feature proteins that might have supported a prebiotic polypeptide world but nothing indicates that RNA world ever was.
  Bioessays, 32, 866-871.  
20852642 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: 2xfz 2xg0 2xg1 2xg2
20876130 D.Bulkley, C.A.Innis, G.Blaha, and T.A.Steitz (2010).
Revisiting the structures of several antibiotics bound to the bacterial ribosome.
  Proc Natl Acad Sci U S A, 107, 17158-17163.
PDB codes: 3oge 3ogy 3oh5 3oh7 3ohc 3ohd 3ohj 3ohk 3ohy 3ohz 3oi0 3oi1 3oi2 3oi3 3oi4 3oi5
20525967 D.Graber, H.Moroder, J.Steger, K.Trappl, N.Polacek, and R.Micura (2010).
Reliable semi-synthesis of hydrolysis-resistant 3'-peptidyl-tRNA conjugates containing genuine tRNA modifications.
  Nucleic Acids Res, 38, 6796-6802.  
20421507 H.Jin, A.C.Kelley, D.Loakes, and V.Ramakrishnan (2010).
Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release.
  Proc Natl Acad Sci U S A, 107, 8593-8598.
PDB codes: 2x9r 2x9s 2x9t 2x9u
20377916 H.S.Bernhardt, and W.P.Tate (2010).
The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA?
  Biol Direct, 5, 16.  
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.  
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
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.  
20974910 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: 3iz5 3iz6 3iz7 3iz9 3izr
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.  
20676057 N.Vázquez-Laslop, H.Ramu, D.Klepacki, K.Kannan, and A.S.Mankin (2010).
The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide.
  EMBO J, 29, 3108-3117.  
20427512 P.C.Whitford, P.Geggier, R.B.Altman, S.C.Blanchard, J.N.Onuchic, and K.Y.Sanbonmatsu (2010).
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.
  RNA, 16, 1196-1204.  
19914248 P.Khade, and S.Joseph (2010).
Functional interactions by transfer RNAs in the ribosome.
  FEBS Lett, 584, 420-426.  
20453830 S.Granneman, E.Petfalski, A.Swiatkowska, and D.Tollervey (2010).
Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking.
  EMBO J, 29, 2026-2036.  
20511136 X.Agirrezabala, and J.Frank (2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
  Hum Genomics, 4, 226-237.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
20005802 C.Neubauer, Y.G.Gao, K.R.Andersen, C.M.Dunham, A.C.Kelley, J.Hentschel, K.Gerdes, V.Ramakrishnan, and D.E.Brodersen (2009).
The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.
  Cell, 139, 1084-1095.
PDB codes: 3kha 3kiq 3kir 3kis 3kit 3kiu 3kiw 3kix 3kiy
19696344 G.Blaha, R.E.Stanley, and T.A.Steitz (2009).
Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
  Science, 325, 966-970.
PDB codes: 3huw 3hux 3huy 3huz
19938030 M.Sprinzl, and V.A.Erdmann (2009).
Protein biosynthesis on ribosomes in molecular resolution: nobel prize for chemistry 2009 goes to three chemical biologists.
  Chembiochem, 10, 2851-2853.  
19833920 T.M.Schmeing, R.M.Voorhees, A.C.Kelley, Y.G.Gao, F.V.Murphy, J.R.Weir, and V.Ramakrishnan (2009).
The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.
  Science, 326, 688-694.
PDB codes: 2wrn 2wro 2wrq 2wrr
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
19833919 Y.G.Gao, M.Selmer, C.M.Dunham, A.Weixlbaumer, A.C.Kelley, and V.Ramakrishnan (2009).
The structure of the ribosome with elongation factor G trapped in the posttranslocational state.
  Science, 326, 694-699.
PDB codes: 2wri 2wrj 2wrk 2wrl
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be 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 codes are shown on the right.

 

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