4C0S | pdb_00004c0s

Mammalian translation elongation factor eEF1A2

• PDB DOI: https://doi.org/10.2210/pdb4C0S/pdb

• Classification: TRANSLATION
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2013-08-07 Released: 2014-08-27 
• Deposition Author(s): Crepin, T., Shalak, V.F., Yaremchuk, A.D., Vlasenko, D.O., McCarthy, A.A., Negrutskii, B.S., Tukalo, M.A., El'skaya, A.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.256 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Mammalian Translation Elongation Factor Eef1A2: X-Ray Structure and New Features of Gdp/GTP Exchange Mechanism in Higher Eukaryotes

Crepin, T., Mccarthy, A., Negrutskii, A., Shalak, V.F., Tukalo, V., Vlasenko, D.O., Yaremchuk, A.D.

(2014) Nucleic Acids Res 42: 12939

• PubMed: 25326326 
• DOI: https://doi.org/10.1093/nar/gku974
• Primary Citation Related Structures: 
  4C0S


• PubMed Abstract: 
  

  Eukaryotic elongation factor eEF1A transits between the GTP- and GDP-bound conformations during the ribosomal polypeptide chain elongation. eEF1A*GTP establishes a complex with the aminoacyl-tRNA in the A site of the 80S ribosome. Correct codon-anticodon recognition triggers GTP hydrolysis, with subsequent dissociation of eEF1A*GDP from the ribosome. The structures of both the 'GTP'- and 'GDP'-bound conformations of eEF1A are unknown. Thus, the eEF1A-related ribosomal mechanisms were anticipated only by analogy with the bacterial homolog EF-Tu. Here, we report the first crystal structure of the mammalian eEF1A2*GDP complex which indicates major differences in the organization of the nucleotide-binding domain and intramolecular movements of eEF1A compared to EF-Tu. Our results explain the nucleotide exchange mechanism in the mammalian eEF1A and suggest that the first step of eEF1A*GDP dissociation from the 80S ribosome is the rotation of the nucleotide-binding domain observed after GTP hydrolysis.

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Organizational Affiliation: 
• University of Grenoble Alpes, UVHCI, F-38000 Grenoble, France CNRS, UVHCI, F-38000 Grenoble, France Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France.
State Key laboratory of Molecular and Cellular Biology, Institute of Molecular Biology and Genetics, 150 Zabolotnogo str., Kiev 03680, Ukraine.
State Key laboratory of Molecular and Cellular Biology, Institute of Molecular Biology and Genetics, 150 Zabolotnogo str., Kiev 03680, Ukraine European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042 France.
Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042 France.
State Key laboratory of Molecular and Cellular Biology, Institute of Molecular Biology and Genetics, 150 Zabolotnogo str., Kiev 03680, Ukraine [e-mail].
State Key laboratory of Molecular and Cellular Biology, Institute of Molecular Biology and Genetics, 150 Zabolotnogo str., Kiev 03680, Ukraine [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 102.35 kDa 
• Atom Count: 6,951 
• Modeled Residue Count: 893 
• Deposited Residue Count: 926 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELONGATION FACTOR 1-ALPHA 2	A, B	463	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for Q71V39 (Oryctolagus cuniculus) Explore Q71V39  Go to UniProtKB:  Q71V39

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], E [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.256 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.37	α = 90
b = 135.37	β = 90
c = 304.62	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Crepin, T., Shalak, V.F., Yaremchuk, A.D., Vlasenko, D.O., McCarthy, A.A., Negrutskii, B.S., Tukalo, M.A., El'skaya, A.V.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2014-10-29
  Changes: Database references
• Version 1.2: 2014-11-26
  Changes: Database references
• Version 1.3: 2017-01-25
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary