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- PDB-2b7b: Yeast guanine nucleotide exchange factor eEF1Balpha K205A mutant ... -

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Basic information

Entry
Database: PDB / ID: 2b7b
TitleYeast guanine nucleotide exchange factor eEF1Balpha K205A mutant in complex with eEF1A and GDP
Components
  • Elongation factor 1-alpha
  • elongation factor-1 beta
KeywordsTRANSLATION / G-protein-GEF complex / eEF1A / eEF1Balpha
Function / homology
Function and homology information


Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / melatonin binding / negative regulation of actin filament bundle assembly / HSF1 activation / regulation of translational termination / tRNA export from nucleus / fungal-type vacuole membrane / Protein methylation / negative regulation of protein phosphorylation ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / melatonin binding / negative regulation of actin filament bundle assembly / HSF1 activation / regulation of translational termination / tRNA export from nucleus / fungal-type vacuole membrane / Protein methylation / negative regulation of protein phosphorylation / actin filament bundle assembly / translational elongation / translation elongation factor activity / negative regulation of protein kinase activity / Neutrophil degranulation / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / maintenance of translational fidelity / actin filament binding / GDP binding / regulation of translation / ribosome binding / cytoskeleton / ribosome / translation / GTPase activity / protein kinase binding / GTP binding / mitochondrion / cytoplasm / cytosol
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'-DIPHOSPHATE / Elongation factor 1-alpha / Elongation factor 1-beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPittman, Y.R. / Valente, L. / Jeppesen, M.G. / Andersen, G.R. / Patel, S. / Kinzy, T.G.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Mg2+ and a key lysine modulate exchange activity of eukaryotic translation elongation factor 1B alpha
Authors: Pittman, Y.R. / Valente, L. / Jeppesen, M.G. / Andersen, G.R. / Patel, S. / Kinzy, T.G.
#1: 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.
#2: 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.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor 1-alpha
B: elongation factor-1 beta
A: GUANOSINE-5'-DIPHOSPHATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9693
Polymers60,5252
Non-polymers4431
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-17 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.90, 91.23, 93.47
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit consists of one molecule each of eF1A and eEF1Balpha

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Components

#1: Protein Elongation factor 1-alpha / EF-1-alpha / Translation elongation factor 1A / Eukaryotic elongation factor 1A / eEF1A / Elongation Factor 1A


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 / EF-1-beta / Translation elongation factor 1B alpha / Eukaryotic elongation factor 1Balpha / ...EF-1-beta / Translation elongation factor 1B alpha / Eukaryotic elongation factor 1Balpha / eEF1Balpha / Elongation Factor 1Balpha


Mass: 10414.727 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: K1205A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TEF5 / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32471
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 12% PEG 2000 MME, 100mM Tris-Cl pH 7.6, 100mM KCl, 3mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 9, 2002 / Details: Three-segment Pt-coated toroidal mirrors
RadiationMonochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 17083 / Num. obs: 17083 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 1.4 / % possible all: 90.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD entry 1F60

1f60


Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.291 980 Random
Rwork0.22 --
all0.224 16678 -
obs0.224 15698 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 28 268 4383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4

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