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- PDB-1n0v: Crystal structure of elongation factor 2 -

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Basic information

Entry
Database: PDB / ID: 1n0v
TitleCrystal structure of elongation factor 2
ComponentsElongation factor 2
KeywordsTRANSLATION / G-protein cis-proline
Function / homology
Function and homology information


Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / maintenance of translational fidelity / protein-folding chaperone binding / ribosome binding ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / maintenance of translational fidelity / protein-folding chaperone binding / ribosome binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol
Similarity search - Function
Yeast translation eEF2 (G' domain) / Yeast translation eEF2 (G' domain) / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Ribosomal Protein S5; domain 2 - #10 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation factors / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV ...Yeast translation eEF2 (G' domain) / Yeast translation eEF2 (G' domain) / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Ribosomal Protein S5; domain 2 - #10 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation factors / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal Protein S5; domain 2 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Alpha-Beta Complex / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsJoergensen, R. / Ortiz, P.A. / Carr-Schmid, A. / Nissen, P. / Kinzy, T.G. / Andersen, G.R.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase.
Authors: Joergensen, R. / Ortiz, P.A. / Carr-Schmid, A. / Nissen, P. / Kinzy, T.G. / Andersen, G.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Purification and Crystallization of the yeast elongation factor eEF2
Authors: Joergensen, R. / Carr-Schmid, A. / Ortiz, P.A. / Kinzy, T.G. / Andersen, G.R.
History
DepositionOct 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Elongation factor 2
D: Elongation factor 2


Theoretical massNumber of molelcules
Total (without water)186,8142
Polymers186,8142
Non-polymers00
Water00
1
C: Elongation factor 2


Theoretical massNumber of molelcules
Total (without water)93,4071
Polymers93,4071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Elongation factor 2


Theoretical massNumber of molelcules
Total (without water)93,4071
Polymers93,4071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.835, 114.546, 177.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe molecule functions as a monomer

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Components

#1: Protein Elongation factor 2 / EF-2


Mass: 93407.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growMethod: vapor diffusion / pH: 7.2
Details: PEG8K, Hepes, ethylene glycol; magnesium chloride, GDP, EDTA, DTT, pH 7.2, VAPOR DIFFUSION, temperature 100K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop
Details: Joergensen, R., (2002) Acta Crystallogr., Sect.D, 58, 712.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMHEPES-NaOH1droppH7.2
275 mM1dropKCl
35 mM1dropMgCl2
40.5 mMEDTA1drop
50.5 mMdithiothreitol1drop
61 mMGDP1drop
74.5 mg/mlprotein1drop
80.1 MHEPES1reservoirpH7.2
95 %ethylene glycol1reservoir
103 mMdithiothreitol1reservoir
110.9 mM1reservoirNaN3
127-9 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.038 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. all: 47695 / Num. obs: 45917 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 39.1
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.316 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 30 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of eEF2-sordarin complex

Resolution: 2.85→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 1101 random
Rwork0.232 --
all0.233 47695 -
obs0.233 45917 -
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12838 0 0 0 12838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_bond_d0.008
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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