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- PDB-1g7c: YEAST EEF1A:EEF1BA IN COMPLEX WITH GDPNP -

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Basic information

Entry
Database: PDB / ID: 1g7c
TitleYEAST EEF1A:EEF1BA IN COMPLEX WITH GDPNP
Components
  • ELONGATION FACTOR 1-ALPHA
  • ELONGATION FACTOR 1-BETA
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 / melatonin binding / regulation of translational termination / HSF1 activation / tRNA export from nucleus / fungal-type vacuole membrane / Protein methylation / actin filament bundle assembly ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / melatonin binding / regulation of translational termination / HSF1 activation / tRNA export from nucleus / fungal-type vacuole membrane / Protein methylation / actin filament bundle assembly / negative regulation of protein phosphorylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / negative regulation of protein kinase activity / maintenance of translational fidelity / actin filament binding / GDP binding / ribosome binding / cytoskeleton / ribosome / translation / GTPase activity / protein kinase binding / GTP 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 / : / Nuclear-export cofactor Arc1p / : / GTP-eEF1A C-terminal domain-like / : / Ribosomal protein S6/Translation elongation factor EF1B / 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. / Glutathione S-transferase, C-terminal domain superfamily / 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. / Translation elongation factor EF1B/ribosomal protein S6 / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / 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
GUANOSINE-5'-MONOPHOSPHATE / Elongation factor 1-alpha / Elongation factor 1-beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsAndersen, G.R. / Valente, L. / Pedersen, L. / Kinzy, T.G. / Nyborg, J.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex.
Authors: Andersen, G.R. / Valente, L. / Pedersen, L. / Kinzy, T.G. / Nyborg, J.
#1: Journal: to be published
Title: Structural Basis for Nucleotide Exchange and Competition with tRNA in the Yeast Elongation Factor Complex eEF1A:eEF1Ba
Authors: Andersen, G.R. / Pedersen, L. / Valente, L. / Kinzy, T.G. / Nyborg, J.
History
DepositionNov 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1-ALPHA
B: ELONGATION FACTOR 1-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9473
Polymers60,5832
Non-polymers3631
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-13 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.641, 90.433, 92.413
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ELONGATION FACTOR 1-ALPHA / EEF1A


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


Mass: 10472.829 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: TKY331 / Gene: TEF5 / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / Strain (production host): 834 DE3 / References: UniProt: P32471
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: mmE 2K, Tris, Hepes, KCl, DTT, GDPNP, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
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: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 34086 / Num. obs: 33704 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.9
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 5.2 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1f60

1f60


Resolution: 2.05→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh & huber
RfactorNum. reflectionSelection details
Rfree0.231 1801 random
Rwork0.208 --
all0.209 33704 -
obs0.209 33380 -
Displacement parametersBiso mean: 21.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 24 448 4566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.08
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.74
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.08
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.74

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