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PDBsum entry 2wri

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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
2wri
Jmol
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. *
667 a.a. *
DNA/RNA
Ligands
FUA
GDP
Metals
_MG
_ZN ×4
* Residue conservation analysis
PDB id:
2wri
Name: Ribosome
Title: The structure of the ribosome with elongation factor g trapped in the post-translocational state (part 1 of 4).
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 - mrc - msaw1. Atcc: 27634. Escherichia coli. Organism_taxid: 83333. Strain: k12. Synthetic: yes. Atcc: 27634
Resolution:
3.60Å     R-factor:   0.227     R-free:   0.260
Authors: Y.-G.Gao,M.Selmer,C.M.Dunham,A.Weixlbaumer,A.C.Kelley, V.Ramakrishnan
Key ref:
Y.G.Gao et al. (2009). The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science, 326, 694-699. PubMed id: 19833919 DOI: 10.1126/science.1179709
Date:
01-Sep-09     Release date:   20-Oct-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  30S ribosomal protein S3
Seq:
Struc:
239 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
Seq:
Struc:
209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
Seq:
Struc:
162 a.a.
151 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  30S ribosomal protein S9
Seq:
Struc:
128 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10
Seq:
Struc:
105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
Seq:
Struc:
132 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ1  (RS14Z_THET8) -  30S ribosomal protein S14 type Z
Seq:
Struc:
61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16
Seq:
Struc:
88 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP7  (RS17_THET8) -  30S ribosomal protein S17
Seq:
Struc:
105 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
Seq:
Struc:
88 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19
Seq:
Struc:
93 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  30S ribosomal protein S20
Seq:
Struc:
106 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SIH3  (RSHX_THET8) -  30S ribosomal protein Thx
Seq:
Struc:
27 a.a.
25 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN5  (EFG_THET8) -  Elongation factor G
Seq:
Struc:
 
Seq:
Struc:
691 a.a.
667 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     translation   3 terms 
  Biochemical function     structural constituent of ribosome     12 terms  

 

 
DOI no: 10.1126/science.1179709 Science 326:694-699 (2009)
PubMed id: 19833919  
 
 
The structure of the ribosome with elongation factor G trapped in the posttranslocational state.
Y.G.Gao, M.Selmer, C.M.Dunham, A.Weixlbaumer, A.C.Kelley, V.Ramakrishnan.
 
  ABSTRACT  
 
Elongation factor G (EF-G) is a guanosine triphosphatase (GTPase) that plays a crucial role in the translocation of transfer RNAs (tRNAs) and messenger RNA (mRNA) during translation by the ribosome. We report a crystal structure refined to 3.6 angstrom resolution of the ribosome trapped with EF-G in the posttranslocational state using the antibiotic fusidic acid. Fusidic acid traps EF-G in a conformation intermediate between the guanosine triphosphate and guanosine diphosphate forms. The interaction of EF-G with ribosomal elements implicated in stimulating catalysis, such as the L10-L12 stalk and the L11 region, and of domain IV of EF-G with the tRNA at the peptidyl-tRNA binding site (P site) and with mRNA shed light on the role of these elements in EF-G function. The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure.
 
  Selected figure(s)  
 
Figure 1.
View larger version (41K): [in this window] [in a new window] Fig. 1. Unbiased difference Fourier electron density maps for (A) EF-G and (B) the ligands fusidic acid (FUS) and GDP with its coordinated Mg^2+ ion in the ribosome. All figures were made by using PyMol (48).
Figure 5.
View larger version (30K): [in this window] [in a new window] Fig. 5. Fusidic acid bound to EF-G in the ribosome. (A) Interactions of fusidic acid in a pocket lined by domains of EF-G, showing amino acids whose mutation gives rise to fusidic acid resistance. (B) A superposition of switch I from the GTP form of EF-G-2 (13) shows it would clash with fusidic acid. (C) Conformational changes between the fusidic acid–bound structure compared with the GDP-bound form of EF-G in isolation [2BM0 from ref. (19)] (gray). F90, switch II of the G domain, and domain III are all in a conformation that is different from the GDP form of EF-G.
 
  The above figures are reprinted by permission from the AAAs: Science (2009, 326, 694-699) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23150038 D.Dulin, J.Lipfert, M.C.Moolman, and N.H.Dekker (2012).
Studying genomic processes at the single-molecule level: introducing the tools and applications.
  Nat Rev Genet, 14, 9.  
22622583 D.J.Ramrath, H.Yamamoto, K.Rother, D.Wittek, M.Pech, T.Mielke, J.Loerke, P.Scheerer, P.Ivanov, Y.Teraoka, O.Shpanchenko, K.H.Nierhaus, and C.M.Spahn (2012).
The complex of tmRNA-SmpB and EF-G on translocating ribosomes.
  Nature, 485, 526-529.
PDB codes: 3j18 3j19
22902368 L.Wang, A.Pulk, M.R.Wasserman, M.B.Feldman, R.B.Altman, J.H.Doudna Cate, and S.C.Blanchard (2012).
Allosteric control of the ribosome by small-molecule antibiotics.
  Nat Struct Mol Biol, 19, 957-963.
PDB codes: 4gaq 4gar 4gas 4gau
22407015 L.Wang, F.Yang, D.Zhang, Z.Chen, R.M.Xu, K.H.Nierhaus, W.Gong, and Y.Qin (2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
  Nat Struct Mol Biol, 19, 403-410.  
22525755 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.  
22358840 T.Becker, S.Franckenberg, S.Wickles, C.J.Shoemaker, A.M.Anger, J.P.Armache, H.Sieber, C.Ungewickell, O.Berninghausen, I.Daberkow, A.Karcher, M.Thomm, K.P.Hopfner, R.Green, and R.Beckmann (2012).
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
  Nature, 482, 501-506.
PDB codes: 3j15 3j16
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
22002225 B.S.Shin, J.R.Kim, S.E.Walker, J.Dong, J.R.Lorsch, and T.E.Dever (2011).
Initiation factor eIF2γ promotes eIF2-GTP-Met-tRNAi(Met) ternary complex binding to the 40S ribosome.
  Nat Struct Mol Biol, 18, 1227-1234.  
21539788 C.Y.Liu, M.T.Qureshi, and T.H.Lee (2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
  Biophys J, 100, 2201-2208.  
21546625 D.J.Farrell, M.Castanheira, and I.Chopra (2011).
Characterization of global patterns and the genetics of fusidic acid resistance.
  Clin Infect Dis, 52, S487-S492.  
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.  
21097998 G.C.Atkinson, and S.L.Baldauf (2011).
Evolution of elongation factor g and the origins of mitochondrial and chloroplast forms.
  Mol Biol Evol, 28, 1281-1292.  
21552257 J.A.Cruz, and E.Westhof (2011).
Sequence-based identification of 3D structural modules in RNA with RMDetect.
  Nat Methods, 8, 513-519.  
21152913 K.Kulczycka, M.Długosz, and J.Trylska (2011).
Molecular dynamics of ribosomal elongation factors G and Tu.
  Eur Biophys J, 40, 289-303.  
21453772 M.J.Han, H.Cimen, J.L.Miller-Lee, H.Koc, and E.C.Koc (2011).
Purification of human mitochondrial ribosomal L7/L12 stalk proteins and reconstitution of functional hybrid ribosomes in Escherichia coli.
  Protein Expr Purif, 78, 48-54.  
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.  
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.  
22020300 P.K.Khade, and S.Joseph (2011).
Messenger RNA interactions in the decoding center control the rate of translocation.
  Nat Struct Mol Biol, 18, 1300-1302.  
21119709 P.Smits, H.Antonicka, P.M.van Hasselt, W.Weraarpachai, W.Haller, M.Schreurs, H.Venselaar, R.J.Rodenburg, J.A.Smeitink, and L.P.van den Heuvel (2011).
Mutation in subdomain G' of mitochondrial elongation factor G1 is associated with combined OXPHOS deficiency in fibroblasts but not in muscle.
  Eur J Hum Genet, 19, 275-279.  
21546624 R.N.Jones, R.E.Mendes, H.S.Sader, and M.Castanheira (2011).
In vitro antimicrobial findings for fusidic acid tested against contemporary (2008-2009) gram-positive organisms collected in the United States.
  Clin Infect Dis, 52, S477-S486.  
21378964 T.M.Schmeing, R.M.Voorhees, A.C.Kelley, and V.Ramakrishnan (2011).
How mutations in tRNA distant from the anticodon affect the fidelity of decoding.
  Nat Struct Mol Biol, 18, 432-436.
PDB codes: 2y0u 2y0v 2y0w 2y0x 2y0y 2y0z 2y10 2y11 2y12 2y13 2y14 2y15 2y16 2y17 2y18 2y19
  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
21124459 A.H.Ratje, J.Loerke, A.Mikolajka, M.Brünner, P.W.Hildebrand, A.L.Starosta, A.Dönhöfer, S.R.Connell, P.Fucini, T.Mielke, P.C.Whitford, J.N.Onuchic, Y.Yu, K.Y.Sanbonmatsu, R.K.Hartmann, P.A.Penczek, D.N.Wilson, and C.M.Spahn (2010).
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
  Nature, 468, 713-716.
PDB codes: 2xsy 2xtg 2xux 2xuy
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.  
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.  
20558545 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: 3m6u 3m6v 3m6w 3m6x
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.  
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.  
20033061 J.B.Munro, R.B.Altman, C.S.Tung, K.Y.Sanbonmatsu, and S.C.Blanchard (2010).
A fast dynamic mode of the EF-G-bound ribosome.
  EMBO J, 29, 770-781.  
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.  
20670889 K.Y.Lo, Z.Li, C.Bussiere, S.Bresson, E.M.Marcotte, and A.W.Johnson (2010).
Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit.
  Mol Cell, 39, 196-208.  
20215430 L.García-Ortega, E.Alvarez-García, J.G.Gavilanes, A.Martínez-del-Pozo, and S.Joseph (2010).
Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding.
  Nucleic Acids Res, 38, 4108-4119.  
21172658 M.M.Golas, B.Sander, S.Bessonov, M.Grote, E.Wolf, B.Kastner, H.Stark, and R.Lührmann (2010).
3D cryo-EM structure of an active step I spliceosome and localization of its catalytic core.
  Mol Cell, 40, 927-938.  
20348921 N.Clementi, A.Chirkova, B.Puffer, R.Micura, and N.Polacek (2010).
Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation.
  Nat Chem Biol, 6, 344-351.  
  21048002 O.K.Kamneva, D.A.Liberles, and N.L.Ward (2010).
Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method.
  Genome Biol Evol, 2, 870-886.  
20534490 S.Kurata, K.H.Nielsen, S.F.Mitchell, J.R.Lorsch, A.Kaji, and H.Kaji (2010).
Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP.
  Proc Natl Acad Sci U S A, 107, 10854-10859.  
20393556 S.Uemura, C.E.Aitken, J.Korlach, B.A.Flusberg, S.W.Turner, and J.D.Puglisi (2010).
Real-time tRNA transit on single translating ribosomes at codon resolution.
  Nature, 464, 1012-1017.  
21187014 X.Liu, S.R.Rodermel, and F.Yu (2010).
A var2 leaf variegation suppressor locus, SUPPRESSOR OF VARIEGATION3, encodes a putative chloroplast translation elongation factor that is important for chloroplast development in the cold.
  BMC Plant Biol, 10, 287.  
20718859 Y.Chen, R.K.Koripella, S.Sanyal, and M.Selmer (2010).
Staphylococcus aureus elongation factor G--structure and analysis of a target for fusidic acid.
  FEBS J, 277, 3789-3803.
PDB code: 2xex
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
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.