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- PDB-1f60: CRYSTAL STRUCTURE OF THE YEAST ELONGATION FACTOR COMPLEX EEF1A:EEF1BA -

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Basic information

Entry
Database: PDB / ID: 1f60
TitleCRYSTAL STRUCTURE OF THE YEAST ELONGATION FACTOR COMPLEX EEF1A:EEF1BA
Components
  • ELONGATION FACTOR EEF1A
  • ELONGATION FACTOR EEF1BA
KeywordsTRANSLATION / protein-protein complex
Function / homology
Function and homology information


Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / HSF1 activation / melatonin binding / regulation of translational termination / tRNA export from nucleus / Protein methylation / fungal-type vacuole membrane / translational elongation ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / HSF1 activation / melatonin binding / regulation of translational termination / tRNA export from nucleus / Protein methylation / fungal-type vacuole membrane / translational elongation / actin filament bundle assembly / translation elongation factor activity / Neutrophil degranulation / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / negative regulation of protein phosphorylation / maintenance of translational fidelity / negative regulation of protein kinase activity / GDP binding / actin filament binding / ribosome binding / cytoskeleton / ribosome / translation / GTPase activity / GTP binding / protein kinase binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / : / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain ...Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / : / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain / EF-1 guanine nucleotide exchange domain / Translation elongation factor EF1A, eukaryotic/archaeal / Ribosomal protein S6/Translation elongation factor EF1B / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Glutathione S-transferase, C-terminal domain superfamily / 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. / Translation elongation factor EF1B/ribosomal protein S6 / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / 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
Elongation factor 1-alpha / Elongation factor 1-beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 Å
AuthorsAndersen, G.R. / Pedersen, L. / Valente, L. / Kinzy, T.G. / Nyborg, J.
Citation
Journal: Mol.Cell / Year: 2000
Title: Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha.
Authors: Andersen, G.R. / Pedersen, L. / Valente, L. / Chatterjee, I. / Kinzy, T.G. / Kjeldgaard, M. / Nyborg, J.
#1: Journal: Structure / Year: 1999
Title: The Solution Structure of the Guanine Nucleotide Exchange Domain of Human Elongation Factor 1beta Reveals a Striking Resemblance to that of EF-Ts from Escherichia coli
Authors: Perez, J.M. / Siegal, G. / Kriek, J. / Hard, K. / Dijk, J. / Canters, G.W. / Moeller, W.
History
DepositionJun 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 EEF1A
B: ELONGATION FACTOR EEF1BA


Theoretical massNumber of molelcules
Total (without water)60,5832
Polymers60,5832
Non-polymers00
Water13,205733
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-12 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.850, 91.810, 92.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ELONGATION FACTOR EEF1A


Mass: 50110.621 Da / Num. of mol.: 1 / Fragment: EEF1A / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02994
#2: Protein ELONGATION FACTOR EEF1BA


Mass: 10472.829 Da / Num. of mol.: 1 / Fragment: EEF1BA, CATALYTICAL C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET11D / Production host: Escherichia coli (E. coli) / References: UniProt: P32471
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: mmE 2000, Tris, Hepes, KCl, DTT, NaAzid, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 4K
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.2
Details: Pedersen, L.P., (2000) Acta Crystallogr., D57, 159.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMHEPES1drop
3100 mM1dropKCl
40.5 mMdithiothreitol1drop
5100 mM1reservoirKCl
6100 mMTris-HCl1reservoir
73 mMdithiothreitol1reservoir
815-18 %PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.67→20 Å / Num. all: 65533 / Num. obs: 65533 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 36.1
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.155 / Num. unique all: 5881 / % possible all: 93.5
Reflection
*PLUS

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.67→20 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: engh & huber in arp_protin.doc
Details: Refmac conjugate direction method
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3217 -random
Rwork0.187 ---
all0.189 63533 --
obs0.189 63533 99.3 %-
Refinement stepCycle: LAST / Resolution: 1.67→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 0 733 4824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.6
X-RAY DIFFRACTIONp_bond_d0.012
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 1.6

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