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- PDB-1n0u: Crystal structure of yeast elongation factor 2 in complex with so... -

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Basic information

Entry
Database: PDB / ID: 1n0u
TitleCrystal structure of yeast elongation factor 2 in complex with sordarin
ComponentsElongation factor 2EEF2
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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / protein-folding chaperone binding / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / 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 / Translation factors / EF-G domain III/V-like / Ribosomal Protein S5; domain 2 / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / 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
Chem-SO1 / Elongation factor 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 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: Jorgensen, 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 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9022
Polymers93,4071
Non-polymers4951
Water8,899494
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.960, 150.830, 65.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsthe molecule functions as a monomer

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Components

#1: Protein Elongation factor 2 / EEF2 / EF-2


Mass: 93407.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324
#2: Chemical ChemComp-SO1 / [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID / SORDARIN


Mass: 494.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: PEG8K, ethylene glycol, Hepes, KCl, magnesium chloride, edta, dtt, gdp, pH 7.2, VAPOR DIFFUSION, temperature 20K
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 2.12→31 Å / Num. all: 67778 / Num. obs: 66427 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.062 / Net I/σ(I): 34.3
Reflection shellResolution: 2.12→2.23 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.7 / % possible all: 94.1
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 98.3 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.12→31 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1953 -random
Rwork0.236 ---
all0.239 67778 --
obs0.239 66427 98 %-
Refinement stepCycle: LAST / Resolution: 2.12→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6375 0 35 494 6904
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_bond_d0.007
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 64474 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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