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- PDB-2npf: Structure of eEF2 in complex with moriniafungin -

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Basic information

Entry
Database: PDB / ID: 2npf
TitleStructure of eEF2 in complex with moriniafungin
ComponentsElongation factor 2EEF2
KeywordsTRANSLATION / protein-inhibitor complex / G-protein
Function / homology
Function and homology information


Peptide chain elongation / Synthesis of diphthamide-EEF2 / Protein methylation / positive regulation of translational elongation / translational elongation / translation elongation factor activity / Neutrophil degranulation / maintenance of translational fidelity / ribosome binding / ribonucleoprotein complex ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / Protein methylation / positive regulation of translational elongation / translational elongation / translation elongation factor activity / Neutrophil degranulation / maintenance of translational fidelity / ribosome binding / ribonucleoprotein complex / chaperone binding / rRNA binding / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Elongation factor G, domain IV / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus ...Yeast translation eEF2 (G' domain) / Yeast translation eEF2 (G' domain) / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Elongation Factor G, domain II / Elongation Factor G, domain III / Elongation factor G, domain IV / Translation elongation factor EFG/EF2, 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 - #10 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation factors / Ribosomal Protein S5; domain 2 / Elongation factor Tu domain 2 / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translational (tr)-type GTP-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Alpha-Beta Complex / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-MOU / Elongation factor 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSoe, R. / Mosley, R.T. / Andersen, G.R.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2
Authors: Soe, R. / Mosley, R.T. / Justice, M. / Nielsen-Kahn, J. / Shastry, M. / Merrill, A.R. / Andersen, G.R.
History
DepositionOct 27, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor 2
B: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,0826
Polymers186,8142
Non-polymers2,2684
Water0
1
A: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5413
Polymers93,4071
Non-polymers1,1342
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5413
Polymers93,4071
Non-polymers1,1342
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)59.970, 159.120, 112.140
Angle α, β, γ (deg.)90.00, 97.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Elongation factor 2 / EEF2 / EF-2 / Translation elongation factor 2 / Eukaryotic elongation factor 2 / eEF2 / Ribosomal translocase


Mass: 93407.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32324
#2: Chemical ChemComp-MOU / (1S,4R,5R,9S,11S)-2-({[(2S,5R,6R,7R,9S,10R)-2-(7-CARBOXYHEPTYL)-6-HYDROXY-10-METHOXY-9-METHYL-3-OXO-1,4,8-TRIOXASPIRO[4.5]DEC-7-YL]OXY}METHYL)-9-FORMYL-13-ISOPROPYL-5-METHYLTETRACYCLO[7.4.0.02,11.04.8]TRIDEC-12-ENE-1-CARBOXYLIC ACID / MORINIAFUNGIN


Mass: 690.817 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H54O12
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG, ethyleneglycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.089 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 5, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.089 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. all: 46128 / Num. obs: 45908 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.05 / Net I/σ(I): 17.5
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 7223 / Rsym value: 0.27 / % possible all: 98.2

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n0u
Resolution: 2.9→25 Å / Cross valid method: throughput / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1161 -random
Rwork0.23 ---
all0.231 46128 --
obs0.231 45908 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12731 0 154 0 12885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.49

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