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PDBsum entry 2ix3

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protein ligands Protein-protein interface(s) links
Translation PDB id
2ix3
Jmol
Contents
Protein chains
973 a.a. *
Ligands
SO4 ×11
* Residue conservation analysis
PDB id:
2ix3
Name: Translation
Title: Structure of yeast elongation factor 3
Structure: Elongation factor 3. Chain: a, b. Fragment: residues 1-980. Synonym: ef-3a, ef-3, translation elongation factor 3a, eukaryotic elongation factor 3, eef3, yeast elongation factor 3. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
Biol. unit: Dimer (from PDB file)
Resolution:
2.70Å     R-factor:   0.216     R-free:   0.269
Authors: C.B.F.Andersen,T.Becker,M.Blau,M.Anand,M.Halic,B.Balar, T.Mielke,T.Boesen,J.S.Pedersen,C.M.T.Spahn,T.G.Kinzy, G.R.Andersen,R.Beckmann
Key ref:
C.B.Andersen et al. (2006). Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Nature, 443, 663-668. PubMed id: 16929303 DOI: 10.1038/nature05126
Date:
06-Jul-06     Release date:   08-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P16521  (EF3A_YEAST) -  Elongation factor 3A
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1044 a.a.
973 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   4 terms 
  Biological process     translation   4 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
DOI no: 10.1038/nature05126 Nature 443:663-668 (2006)
PubMed id: 16929303  
 
 
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
C.B.Andersen, T.Becker, M.Blau, M.Anand, M.Halic, B.Balar, T.Mielke, T.Boesen, J.S.Pedersen, C.M.Spahn, T.G.Kinzy, G.R.Andersen, R.Beckmann.
 
  ABSTRACT  
 
Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aminoacyl-tRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate the clearance of deacyl-tRNA from the E-site. Here we present the crystal structure of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains, with a chromodomain inserted in ABC2. Moreover, we present the cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structures of Saccharomyces cerevisiae eEF3 and nucleotide binding. a, Schematic representation of the eEF3 sequence. See the text for a description of the different domains. Chromo, chromodomain; C-term, carboxy-terminal domain. b, Stereo view of the crystal structure of eEF3–ADP. The nucleotide is shown in ball-and-stick representation. c, Stereo view of the nucleotide-binding site. The electron density of ADP is generated from an omit map contoured at 1.5 (grey) or at 0.8 around the -phosphate (green). d, Three different conformations of eEF3. Left: crystal structure of eEF3. Middle: ATP model of eEF3 constructed using homology to the structure of MJ0796. Right: Cryo-electron microscopy (cryo-EM) reconstruction of eEF3 on the 80S ribosome.
Figure 4.
Figure 4: Model of the role of eEF3 in the fungal elongation cycle. a, The post-state ribosome with a locked E-site tRNA owing to the L1 stalk in the 'in' position and the conformation of the 40S head (Post, locked E). b, Hypothetical initial interaction of eEF3 in the open tandem or intermediate conformation (Post*, locked E). c, Ribosome interaction triggers the ATP-dependent closed tandem formation and high-affinity ribosome binding by eEF3, as observed by cryo-EM (Post*). A conformational switch of the chromodomain stabilizes the L1 stalk in the 'out' position (unlocked E). d, ATP hydrolysis of the closed tandem results in the dissociation of eEF3, E-site opening, and unlocking of the 40S head (Post). Now, eEF1A–GTP–aminoacyl-tRNA can bind and the E-site deacyl-tRNA is released. ATP hydrolysis by eEF3, tRNA release, and A-site loading by eEF1A may take place as a joint event. aatRNA, aminoacyl-tRNA. RSR, ratchet-like subunit rearrangement.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 443, 663-668) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22231402 I.Holdermann, N.H.Meyer, A.Round, K.Wild, M.Sattler, and I.Sinning (2012).
Chromodomains read the arginine code of post-translational targeting.
  Nat Struct Mol Biol, 19, 260-263.
PDB code: 3ui2
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
20122402 A.V.Pisarev, M.A.Skabkin, V.P.Pisareva, O.V.Skabkina, A.M.Rakotondrafara, M.W.Hentze, C.U.Hellen, and T.V.Pestova (2010).
The role of ABCE1 in eukaryotic posttermination ribosomal recycling.
  Mol Cell, 37, 196-210.  
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.  
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
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.  
19117941 J.D.Dinman (2009).
The eukaryotic ribosome: current status and challenges.
  J Biol Chem, 284, 11761-11765.  
19368888 J.Timmins, E.Gordon, S.Caria, G.Leonard, S.Acajjaoui, M.S.Kuo, V.Monchois, and S.McSweeney (2009).
Structural and mutational analyses of Deinococcus radiodurans UvrA2 provide insight into DNA binding and damage recognition by UvrAs.
  Structure, 17, 547-558.
PDB codes: 2vf7 2vf8
19580778 K.Vu, J.Bautos, M.P.Hong, and A.Gelli (2009).
The functional expression of toxic genes: lessons learned from molecular cloning of CCH1, a high-affinity Ca2+ channel.
  Anal Biochem, 393, 234-241.  
19666721 N.Van Dyke, B.F.Pickering, and M.W.Van Dyke (2009).
Stm1p alters the ribosome association of eukaryotic elongation factor 3 and affects translation elongation.
  Nucleic Acids Res, 37, 6116-6125.  
19570978 S.Paytubi, X.Wang, Y.W.Lam, L.Izquierdo, M.J.Hunter, E.Jan, H.S.Hundal, and C.G.Proud (2009).
ABC50 promotes translation initiation in mammalian cells.
  J Biol Chem, 284, 24061-24073.  
18160405 A.Karcher, A.Schele, and K.P.Hopfner (2008).
X-ray structure of the complete ABC enzyme ABCE1 from Pyrococcus abyssi.
  J Biol Chem, 283, 7962-7971.
PDB code: 3bk7
18535149 A.L.Davidson, E.Dassa, C.Orelle, and J.Chen (2008).
Structure, function, and evolution of bacterial ATP-binding cassette systems.
  Microbiol Mol Biol Rev, 72, 317.  
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.  
18606549 J.LeBarron, R.A.Grassucci, T.R.Shaikh, W.T.Baxter, J.Sengupta, and J.Frank (2008).
Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.
  J Struct Biol, 164, 24-32.  
18503003 M.Liu, and A.Gelli (2008).
Elongation factor 3, EF3, associates with the calcium channel Cch1 and targets Cch1 to the plasma membrane in Cryptococcus neoformans.
  Eukaryot Cell, 7, 1118-1126.  
18786405 M.V.Petoukhov, J.B.Vicente, P.B.Crowley, M.A.Carrondo, M.Teixeira, and D.I.Svergun (2008).
Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering.
  Structure, 16, 1428-1436.  
18400176 P.Chandramouli, M.Topf, J.F.Ménétret, N.Eswar, J.J.Cannone, R.R.Gutell, A.Sali, and C.W.Akey (2008).
Structure of the mammalian 80S ribosome at 8.7 A resolution.
  Structure, 16, 535-548.
PDB codes: 2zkq 2zkr
18632761 T.V.Budkevich, A.V.El'skaya, and K.H.Nierhaus (2008).
Features of 80S mammalian ribosome and its subunits.
  Nucleic Acids Res, 36, 4736-4744.  
18667704 V.Di Giacco, V.Márquez, Y.Qin, M.Pech, F.J.Triana-Alonso, D.N.Wilson, and K.H.Nierhaus (2008).
Shine-Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG.
  Proc Natl Acad Sci U S A, 105, 10715-10720.  
17565370 E.P.Plant, P.Nguyen, J.R.Russ, Y.R.Pittman, T.Nguyen, J.T.Quesinberry, T.G.Kinzy, and J.D.Dinman (2007).
Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae.
  PLoS ONE, 2, e517.  
17901157 O.Galkin, A.A.Bentley, S.Gupta, B.A.Compton, B.Mazumder, T.G.Kinzy, W.C.Merrick, M.Hatzoglou, T.V.Pestova, C.U.Hellen, and A.A.Komar (2007).
Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5.
  RNA, 13, 2116-2128.  
17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
  Curr Opin Struct Biol, 17, 302-309.  
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 code is shown on the right.