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- PDB-3ecs: Crystal structure of human eIF2B alpha -

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Basic information

Entry
Database: PDB / ID: 3ecs
TitleCrystal structure of human eIF2B alpha
ComponentsTranslation initiation factor eIF-2B subunit alpha
KeywordsTRANSLATION / eukaryotic translation initiation factor 2Balpha (eIF2Balpha) / guanine nucleotide exchange factor (GEF) / initiation / stress response / Disease mutation / Initiation factor / Protein biosynthesis / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / oligodendrocyte development / response to glucose / translational initiation / translation initiation factor activity / guanyl-nucleotide exchange factor activity / response to peptide hormone / T cell receptor signaling pathway ...eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / oligodendrocyte development / response to glucose / translational initiation / translation initiation factor activity / guanyl-nucleotide exchange factor activity / response to peptide hormone / T cell receptor signaling pathway / response to heat / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor eIF-2B, N-terminal domain / Translation initiation factor eif-2b; domain 2 / : / Translation initiation factor eIF-2B subunit alpha, N-terminal / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...Translation initiation factor eIF-2B, N-terminal domain / Translation initiation factor eif-2b; domain 2 / : / Translation initiation factor eIF-2B subunit alpha, N-terminal / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor eIF2B subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsHiyama, T.B. / Ito, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the alpha subunit of human translation initiation factor 2B
Authors: Hiyama, T.B. / Ito, T. / Imataka, H. / Yokoyama, S.
History
DepositionSep 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translation initiation factor eIF-2B subunit alpha
B: Translation initiation factor eIF-2B subunit alpha
C: Translation initiation factor eIF-2B subunit alpha
D: Translation initiation factor eIF-2B subunit alpha
E: Translation initiation factor eIF-2B subunit alpha
F: Translation initiation factor eIF-2B subunit alpha
G: Translation initiation factor eIF-2B subunit alpha
H: Translation initiation factor eIF-2B subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,02519
Polymers282,0298
Non-polymers99611
Water3,333185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22590 Å2
ΔGint-300 kcal/mol
Surface area91180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.885, 156.394, 138.441
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHOR STATES THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: Protein
Translation initiation factor eIF-2B subunit alpha / eukaryotic translation initiation factor 2B alpha / eIF-2B GDP-GTP exchange factor subunit alpha


Mass: 35253.633 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q14232
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium Citrate buffer(pH 4.5), 0.1M Ammonium Sulfate, 13% polyethylene glycol(PEG) 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2008 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 84757 / Num. obs: 84588 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.181 / Rsym value: 0.181 / Net I/σ(I): 16.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2 / Num. unique all: 4166 / Rsym value: 0.806 / % possible all: 99.2

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Processing

Software
NameClassification
HKL-2000data collection
autoSHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.65→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 4200 -RANDOM
Rwork0.214 ---
all-84757 --
obs-84095 99.2 %-
Displacement parametersBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.11 Å25.78 Å210.89 Å2
2--0 Å2-9.79 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17722 0 51 185 17958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it4.13
X-RAY DIFFRACTIONc_mcangle_it5.96
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.357 682 -
Rwork0.287 --
obs-13120 98.1 %

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