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- PDB-5w2f: Crystal Structure of the C-terminal Domain of Human eIF2D at 1.4 ... -

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Basic information

Entry
Database: PDB / ID: 5w2f
TitleCrystal Structure of the C-terminal Domain of Human eIF2D at 1.4 A resolution
ComponentsEukaryotic translation initiation factor 2D
KeywordsTRANSLATION / Re-initiation / Ribosome / eIF2
Function / homology
Function and homology information


IRES-dependent viral translational initiation / ribosome disassembly / formation of translation preinitiation complex / translation initiation factor activity / intracellular protein transport / signaling receptor activity / nuclear body / RNA binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 2D, SUI1 domain / : / : / Eukaryotic translation initiation factor 2D / Pre-PUA domain / Pre-PUA-like domain / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain ...Eukaryotic translation initiation factor 2D, SUI1 domain / : / : / Eukaryotic translation initiation factor 2D / Pre-PUA domain / Pre-PUA-like domain / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / PUA-like superfamily
Similarity search - Domain/homology
FORMIC ACID / Eukaryotic translation initiation factor 2D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsVaidya, A.T. / Lomakin, I.B. / Joseph, N.N. / Dmitriev, S.E. / Steitz, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30DK034989 United States
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Crystal Structure of the C-terminal Domain of Human eIF2D and Its Implications on Eukaryotic Translation Initiation.
Authors: Vaidya, A.T. / Lomakin, I.B. / Joseph, N.N. / Dmitriev, S.E. / Steitz, T.A.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 2D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2004
Polymers23,0621
Non-polymers1383
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint0 kcal/mol
Surface area11560 Å2
Unit cell
Length a, b, c (Å)50.650, 50.650, 183.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Eukaryotic translation initiation factor 2D / eIF2d / Hepatocellular carcinoma-associated antigen 56 / Ligatin


Mass: 23061.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2D, HCA56, LGTN / Production host: Escherichia coli (E. coli) / References: UniProt: P41214
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 3.5 M Sodium Formate, 100 mM Sodium Acetate pH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→48.83 Å / Num. obs: 47791 / % possible obs: 99.1 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.023 / Rrim(I) all: 0.049 / Net I/σ(I): 14.7 / Num. measured all: 198682 / Scaling rejects: 3
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
1.4-1.423.11.098671621570.50.6741.2970.994.2
7.66-48.8340.03114053540.9970.0170.03640.696.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.22data extraction
SHELXdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→48.83 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.028 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 2259 4.7 %RANDOM
Rwork0.1404 ---
obs0.1419 45498 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.33 Å2 / Biso mean: 29.529 Å2 / Biso min: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å2-0 Å2
2--0.37 Å20 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.4→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 9 228 1818
Biso mean--38.18 46.14 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191651
X-RAY DIFFRACTIONr_bond_other_d0.0020.021587
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9892247
X-RAY DIFFRACTIONr_angle_other_deg0.91333719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9525214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65125.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96615309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.333158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211811
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
X-RAY DIFFRACTIONr_rigid_bond_restr1.50633238
X-RAY DIFFRACTIONr_sphericity_free40.0955118
X-RAY DIFFRACTIONr_sphericity_bonded14.98153315
LS refinement shellResolution: 1.399→1.435 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 153 -
Rwork0.293 3184 -
all-3337 -
obs--95.62 %

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