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- PDB-8dys: Crystal structure of human Eukaryotic translation initiation fact... -

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Basic information

Entry
Database: PDB / ID: 8dys
TitleCrystal structure of human Eukaryotic translation initiation factor 2A (eIF2A)
ComponentsEukaryotic translation initiation factor 2A
KeywordsTRANSLATION / WDR / WD-repeat protein / eIF2A / translation initiation factor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of signal transduction / SREBP signaling pathway / eukaryotic translation initiation factor 2 complex / response to amino acid starvation / translation initiation factor activity / ribosome assembly / ribosome binding / regulation of translation / cytosolic small ribosomal subunit / tRNA binding ...positive regulation of signal transduction / SREBP signaling pathway / eukaryotic translation initiation factor 2 complex / response to amino acid starvation / translation initiation factor activity / ribosome assembly / ribosome binding / regulation of translation / cytosolic small ribosomal subunit / tRNA binding / blood microparticle / cadherin binding / protein phosphorylation / mRNA binding / extracellular space / cytoplasm
Similarity search - Function
Translation initiation factor 2A / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsRighetto, G.L. / Zeng, H. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To Be Published
Title: Crystal structure of human Eukaryotic translation initiation factor 2A (eIF2A)
Authors: Righetto, G.L. / Zeng, H. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionAug 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Eukaryotic translation initiation factor 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4877
Polymers67,2711
Non-polymers2166
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.289, 84.847, 99.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Eukaryotic translation initiation factor 2A / eIF-2A / 65 kDa eukaryotic translation initiation factor 2A


Mass: 67271.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2A, CDA02, MSTP004, MSTP089 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BY44
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.7 Å3/Da / Density % sol: 27.67 % / Mosaicity: 0.16 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 2K, 0.2M Potassium Bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→47.68 Å / Num. obs: 42642 / % possible obs: 98.8 % / Redundancy: 7.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.117 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.847.90.8081967924810.8320.3040.8643.698.1
9-47.646.40.06626184120.9940.0290.07225.399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJ9

3wj9


Resolution: 1.8→47.68 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.826 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 2087 4.9 %RANDOM
Rwork0.1995 ---
obs0.2009 40514 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.62 Å2 / Biso mean: 25.797 Å2 / Biso min: 13.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å2-0 Å20 Å2
2---0.7 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.8→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 17 199 3373
Biso mean--38.34 33.02 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123290
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172898
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.6394500
X-RAY DIFFRACTIONr_angle_other_deg1.3561.5626730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1195412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41823.873142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03815473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.738156
X-RAY DIFFRACTIONr_chiral_restr0.060.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 146 -
Rwork0.237 2922 -
all-3068 -
obs--98.05 %

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