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- PDB-3jui: Crystal Structure of the C-terminal Domain of Human Translation I... -

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Basic information

Entry
Database: PDB / ID: 3jui
TitleCrystal Structure of the C-terminal Domain of Human Translation Initiation Factor eIF2B epsilon Subunit
ComponentsTranslation initiation factor eIF-2B subunit epsilon
KeywordsTRANSLATION / HEAT repeat / guanine nucleotide exchange factor / translation initiation factor / Disease mutation / Initiation factor / Leukodystrophy / Phosphoprotein / Protein biosynthesis
Function / homology
Function and homology information


eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / oligodendrocyte development / astrocyte development / astrocyte differentiation / positive regulation of translational initiation / response to glucose / ovarian follicle development / translational initiation ...eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / oligodendrocyte development / astrocyte development / astrocyte differentiation / positive regulation of translational initiation / response to glucose / ovarian follicle development / translational initiation / translation initiation factor binding / translation initiation factor activity / myelination / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / hippocampus development / response to peptide hormone / T cell receptor signaling pathway / response to heat / positive regulation of apoptotic process / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Translation initiation factor eIF2B subunit epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsWei, J. / Xu, H. / Zhang, C. / Wang, M. / Gao, F. / Gong, W.
CitationJournal: To be published
Title: Crystal Structure of the C-terminal Domain of Human Translation Initiation Factor eIF2B epsilon Subunit
Authors: Wei, J. / Xu, H. / Zhang, C. / Wang, M. / Gao, F. / Gong, W.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4772
Polymers21,3841
Non-polymers921
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.537, 66.082, 136.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 21384.492 Da / Num. of mol.: 1 / Fragment: C-terminal Domain / Mutation: E678G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B5, EIF2BE / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): b834 / References: UniProt: Q13144
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.45 Å3/Da / Density % sol: 49.73 % / Mosaicity: 0.731 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.7
Details: PEG8000, Calcium acetate, Sodium Cocadylate, pH 7.7, vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9796, 0.9794, 0.9600
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97941
30.961
ReflectionRedundancy: 7.1 % / Av σ(I) over netI: 24.08 / Number: 69282 / Rmerge(I) obs: 0.072 / Χ2: 1.32 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 9770 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955097.210.062.2146.3
3.934.9599.510.0531.8856.9
3.443.9310010.0561.4787.1
3.123.4410010.0691.3737.2
2.93.1210010.0821.2857.3
2.732.910010.0941.167.3
2.592.7310010.111.0117.3
2.482.5910010.1271.0447.3
2.382.4810010.1550.9447.4
2.32.3810010.170.8756.8
ReflectionResolution: 2→50 Å / Num. obs: 13260 / % possible obs: 90.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Χ2: 1.202 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.077.40.31311960.868184.1
2.07-2.157.30.25312010.874183.1
2.15-2.257.10.19412080.948183.6
2.25-2.376.80.17612510.966186
2.37-2.526.70.13312690.949189.1
2.52-2.716.70.10213231.009190.7
2.71-2.996.70.0813451.134192.8
2.99-3.426.80.05914131.352196.3
3.42-4.317.80.04614831.517199.9
4.31-508.70.04815711.859199.3

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97822.73-8.43
3 wavelength120.97795.48-7.56
3 wavelength130.88563.93-2.98
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se24.5970.8660.110.0990.718
2Se23.1030.1150.4550.0860.573
3Se34.5980.1230.1590.1740.643
4Se3.0650.3610.2720.0770.362
5Se47.1130.7520.4830.1490.775
Phasing dmFOM : 0.89 / FOM acentric: 0.9 / FOM centric: 0.83 / Reflection: 4376 / Reflection acentric: 3663 / Reflection centric: 713
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-14.970.950.940.9615710750
5.4-8.60.920.940.86620469151
4.3-5.40.930.950.86740609131
3.8-4.30.920.930.86744628116
3.2-3.80.880.890.8113141133181
3-3.20.80.820.6580171784

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→29.16 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.217 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.885 / SU B: 4.527 / SU ML: 0.13 / SU R Cruickshank DPI: 0.219 / SU Rfree: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.206
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.279 661 5 %RANDOM
Rwork0.211 ---
obs0.214 13149 90.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.35 Å2 / Biso mean: 24.42 Å2 / Biso min: 4.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 6 94 1522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221481
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.952001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70424.93577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90915275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.742157
X-RAY DIFFRACTIONr_chiral_restr0.1460.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021115
X-RAY DIFFRACTIONr_mcbond_it1.11.5877
X-RAY DIFFRACTIONr_mcangle_it1.81221409
X-RAY DIFFRACTIONr_scbond_it3.193604
X-RAY DIFFRACTIONr_scangle_it4.4484.5588
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 39 -
Rwork0.212 826 -
all-865 -
obs--83.25 %

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