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PDBsum entry 2p8x

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protein ligands Protein-protein interface(s) links
Translation PDB id
2p8x
Jmol PyMol
Contents
Protein chains
814 a.a. *
35 a.a. *
Ligands
APR
GNP
* Residue conservation analysis
PDB id:
2p8x
Name: Translation
Title: Fitted structure of adpr-eef2 in the 80s:adpr-eef2:gdpnp cryo-em reconstruction
Structure: Elongation factor 2. Chain: t. Synonym: ef-2, translation elongation factor 2, eukaryotic elongation factor 2, eef2, ribosomal translocase. Elongation factor tu-b. Chain: s. Fragment: switch 1 loop. Synonym: ef-tu-b
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Thermus thermophilus. Organism_taxid: 274
Authors: D.J.Taylor,J.Nilsson,A.R.Merrill,G.R.Andersen,P.Nissen, J.Frank
Key ref:
D.J.Taylor et al. (2007). Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. EMBO J, 26, 2421-2431. PubMed id: 17446867 DOI: 10.1038/sj.emboj.7601677
Date:
23-Mar-07     Release date:   08-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P32324  (EF2_YEAST) -  Elongation factor 2
Seq:
Struc:
 
Seq:
Struc:
842 a.a.
814 a.a.*
Protein chain
Pfam   ArchSchema ?
P60339  (EFTU2_THET8) -  Elongation factor Tu-B
Seq:
Struc:
406 a.a.
35 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     translation   5 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
DOI no: 10.1038/sj.emboj.7601677 EMBO J 26:2421-2431 (2007)
PubMed id: 17446867  
 
 
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
D.J.Taylor, J.Nilsson, A.R.Merrill, G.R.Andersen, P.Nissen, J.Frank.
 
  ABSTRACT  
 
On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 in eukaryotes, EF-G in bacteria). We have obtained cryo-EM reconstructions of eukaryotic ribosomes complexed with ADP-ribosylated eEF2 (ADPR-eEF2), before and after GTP hydrolysis, providing a structural basis for analyzing the GTPase-coupled mechanism of translocation. Using the ADP-ribosyl group as a distinct marker, we observe conformational changes of ADPR-eEF2 that are due strictly to GTP hydrolysis. These movements are likely representative of native eEF2 motions in a physiological context and are sufficient to uncouple the mRNA-tRNA complex from two universally conserved bases in the ribosomal decoding center (A1492 and A1493 in Escherichia coli) during translocation. Interpretation of these data provides a detailed two-step model of translocation that begins with the eEF2/EF-G binding-induced ratcheting motion of the small ribosomal subunit. GTP hydrolysis then uncouples the mRNA-tRNA complex from the decoding center so translocation of the mRNA-tRNA moiety may be completed by a head rotation of the small subunit.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Superimposition of the Switch 1 loop from the EF–Tu ternary complex. The Switch 1 loop from the crystal structure of the EF–Tu ternary complex was superimposed onto our quasi-atomic models of eEF2 bound to the ribosome by least-squares alignment of the conserved helix A in domain I of the two structures. The Switch 1 loop from EF–Tu is accommodated by density in the cryo-EM structures of eEF2 in the GTP state (A) and ADPR-eEF2 in the GTP state (B), but the density of ADPR-eEF2 in the GDP state (C) shows that the Switch 1 loop has become disordered after GTP hydrolysis has occurred. Domains of eEF2 and ADPR-eEF2 are color-coded, the Switch 1 loop is colored orange, and GDP is colored black in all three panels. This figure was generated using PyMOL (DeLano, 2002).
Figure 7.
Figure 7 Head rotation of the 40S subunit of the yeast 80S ribosome. Binding of eEF2 induces a subunit rearrangement that involves ratcheting of the SSU with respect to the LSU, as well as head rotations in the SSU. To discriminate the difference induced exclusively by the head rotation, we superimposed the bodies of the SSU from the quasi-atomic models of the pre-translocational (Spahn et al, 2001) and the ratcheted, eEF2-bound (Spahn et al, 2004) 80S ribosomes, by explicit least-squares fitting using the program O (Jones et al, 1991). The SSU of the pre-translocational ribosome with P-site tRNA (PDB ID: 1K5X) is shown in tan, and that of the eEF2-bound ribosome (PDB ID: 1S1H) is shown in blue. Highlighted residues U955 and A1339 are in regions known to interact with ribosome-bound tRNA (Yusupov et al, 2001). This alignment demonstrates that head rotation alone can account for 12–13 Å movements of tRNA during translocation. Similar ratcheting and head rotations have been noted for the SSU of the bacterial ribosome (Schuwirth et al, 2005), suggesting that the mechanism of translocation is conserved.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 2421-2431) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
  21394738 G.Kaul, G.Pattan, and T.Rafeequi (2011).
Eukaryotic elongation factor-2 (eEF2): its regulation and peptide chain elongation.
  Cell Biochem Funct, 29, 227-234.  
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.  
21336521 M.Valle (2011).
Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.
  Eur Biophys J, 40, 589-597.  
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.  
  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
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.  
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.  
20159470 J.F.Flanagan, O.Namy, I.Brierley, and R.J.Gilbert (2010).
Direct observation of distinct A/P hybrid-state tRNAs in translocating ribosomes.
  Structure, 18, 257-264.  
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.  
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.  
20631791 N.Fischer, A.L.Konevega, W.Wintermeyer, M.V.Rodnina, and H.Stark (2010).
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.
  Nature, 466, 329-333.  
21051640 R.M.Voorhees, T.M.Schmeing, A.C.Kelley, and V.Ramakrishnan (2010).
The mechanism for activation of GTP hydrolysis on the ribosome.
  Science, 330, 835-838.
PDB codes: 2xqd 2xqe
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.  
19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
  J Biol Chem, 284, 21103-21119.  
19029250 B.S.Shin, J.R.Kim, M.G.Acker, K.N.Maher, J.R.Lorsch, and T.E.Dever (2009).
rRNA suppressor of a eukaryotic translation initiation factor 5B/initiation factor 2 mutant reveals a binding site for translational GTPases on the small ribosomal subunit.
  Mol Cell Biol, 29, 808-821.  
19536129 C.Ticu, R.Nechifor, B.Nguyen, M.Desrosiers, and K.S.Wilson (2009).
Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome.
  EMBO J, 28, 2053-2065.  
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.  
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
19571367 I.Tinoco, and J.D.Wen (2009).
Simulation and analysis of single-ribosome translation.
  Phys Biol, 6, 25006.  
20004156 J.D.Dinman, and T.G.Kinzy (2009).
Expanding the ribosomal universe.
  Structure, 17, 1547-1548.  
20025794 J.Frank (2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
  Q Rev Biophys, 42, 139-158.  
19716793 M.Tsuboi, H.Morita, Y.Nozaki, K.Akama, T.Ueda, K.Ito, K.H.Nierhaus, and N.Takeuchi (2009).
EF-G2mt is an exclusive recycling factor in mammalian mitochondrial protein synthesis.
  Mol Cell, 35, 502-510.  
19597483 S.H.Sternberg, J.Fei, N.Prywes, K.A.McGrath, and R.L.Gonzalez (2009).
Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling.
  Nat Struct Mol Biol, 16, 861-868.  
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.  
19269332 W.T.Baxter, R.A.Grassucci, H.Gao, and J.Frank (2009).
Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.
  J Struct Biol, 166, 126-132.  
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.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
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.
  Biopolymers, 89, 565-577.  
18285480 J.Botet, M.Rodríguez-Mateos, J.P.Ballesta, J.L.Revuelta, and M.Remacha (2008).
A chemical genomic screen in Saccharomyces cerevisiae reveals a role for diphthamidation of translation elongation factor 2 in inhibition of protein synthesis by sordarin.
  Antimicrob Agents Chemother, 52, 1623-1629.  
18644383 J.Sengupta, J.Nilsson, R.Gursky, M.Kjeldgaard, P.Nissen, and J.Frank (2008).
Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.
  J Mol Biol, 382, 179-187.
PDB codes: 3dny 3dwu
18951096 L.Garcia-Ortega, J.Stephen, and S.Joseph (2008).
Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation.
  Mol Cell, 32, 292-299.  
18274535 R.A.Grassucci, D.Taylor, and J.Frank (2008).
Visualization of macromolecular complexes using cryo-electron microscopy with FEI Tecnai transmission electron microscopes.
  Nat Protoc, 3, 330-339.  
18362332 R.N.Evans, G.Blaha, S.Bailey, and T.A.Steitz (2008).
The structure of LepA, the ribosomal back translocase.
  Proc Natl Acad Sci U S A, 105, 4673-4678.
PDB code: 3cb4
18591673 S.E.Walker, S.Shoji, D.Pan, B.S.Cooperman, and K.Fredrick (2008).
Role of hybrid tRNA-binding states in ribosomal translocation.
  Proc Natl Acad Sci U S A, 105, 9192-9197.  
18462671 S.J.Moran, J.F.Flanagan, O.Namy, D.I.Stuart, I.Brierley, and R.J.Gilbert (2008).
The mechanics of translocation: a molecular "spring-and-ratchet" system.
  Structure, 16, 664-672.  
19180078 T.R.Shaikh, H.Gao, W.T.Baxter, F.J.Asturias, N.Boisset, A.Leith, and J.Frank (2008).
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
  Nat Protoc, 3, 1941-1974.  
18974836 Z.Frankenstein, J.Sperling, R.Sperling, and M.Eisenstein (2008).
FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.
  PLoS ONE, 3, e3594.  
18075576 C.V.Robinson, A.Sali, and W.Baumeister (2007).
The molecular sociology of the cell.
  Nature, 450, 973-982.  
18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
  Proc Natl Acad Sci U S A, 104, 19671-19678.  
18079724 R.A.Grassucci, D.J.Taylor, and J.Frank (2007).
Preparation of macromolecular complexes for cryo-electron microscopy.
  Nat Protoc, 2, 3239-3246.  
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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