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- PDB-1q46: crystal structure of the eIF2 alpha subunit from saccharomyces ce... -

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Basic information

Entry
Database: PDB / ID: 1q46
Titlecrystal structure of the eIF2 alpha subunit from saccharomyces cerevisia
Componentstranslation initiation factor 2 alpha subunit
KeywordsTRANSLATION / initiation factor / eIF2 / phosphorylation site
Function / homology
Function and homology information


Recycling of eIF2:GDP / Cellular response to mitochondrial stress / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2 complex / multi-eIF complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition ...Recycling of eIF2:GDP / Cellular response to mitochondrial stress / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2 complex / multi-eIF complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor activity / translational initiation / cytoplasmic stress granule / ribosome binding / ribosome / RNA binding / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor 2; subunit 1; domain 2 / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / Nucleic acid-binding proteins / S1 RNA binding domain ...Translation initiation factor 2; subunit 1; domain 2 / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / Nucleic acid-binding proteins / S1 RNA binding domain / S1 domain / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2 subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsDhaliwal, S. / Hoffman, D.W.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The crystal structure of the N-terminal region of the alpha subunit of translation initiation factor 2 (eIF2alpha) from Saccharomyces cerevisiae provides a view of the loop containing serine ...Title: The crystal structure of the N-terminal region of the alpha subunit of translation initiation factor 2 (eIF2alpha) from Saccharomyces cerevisiae provides a view of the loop containing serine 51, the target of the eIF2alpha-specific kinases.
Authors: Dhaliwal, S. / Hoffman, D.W.
History
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: translation initiation factor 2 alpha subunit


Theoretical massNumber of molelcules
Total (without water)20,5981
Polymers20,5981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.009, 94.009, 81.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein translation initiation factor 2 alpha subunit / eIF-2- alpha


Mass: 20597.834 Da / Num. of mol.: 1 / Fragment: N-terminal two thirds of eIF2a / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20459

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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: 4.35 Å3/Da / Density % sol: 71.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate (pH=4.6), 1.8-2.5 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8-2.5 Msodium formate11
20.1 Macetate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 2003 / Details: osmium mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.86→20 Å / Num. all: 8830 / Num. obs: 8830 / % possible obs: 99.8 % / Observed criterion σ(F): 2
Reflection shellResolution: 2.86→2.96 Å / Mean I/σ(I) obs: 1.3 / Rsym value: 0.583 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 9935 / % possible obs: 99.5 % / Redundancy: 7.78 % / Num. measured all: 77383 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Rmerge(I) obs: 0.583

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human eIF2 alpha subunit

Resolution: 2.86→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2362 471 random
Rwork0.2181 --
all0.222 8830 -
obs0.222 8830 -
Refinement stepCycle: LAST / Resolution: 2.86→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 0 1441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.2159
LS refinement shellResolution: 2.86→2.96 Å
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.21

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