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- PDB-5b04: Crystal structure of the eukaryotic translation initiation factor... -

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Basic information

Entry
Database: PDB / ID: 5b04
TitleCrystal structure of the eukaryotic translation initiation factor 2B from Schizosaccharomyces pombe
Components
  • (Probable translation initiation factor eIF-2B subunit ...) x 4
  • Translation initiation factor eIF-2B subunit alpha
KeywordsTRANSLATION / Complex
Function / homology
Function and homology information


Recycling of eIF2:GDP / cytoplasmic translational initiation / eukaryotic translation initiation factor 2B complex / regulation of translational initiation / nucleotidyltransferase activity / guanyl-nucleotide exchange factor activity / translation initiation factor binding / translational initiation / translation initiation factor activity / nucleus / cytosol
Armadillo-type fold / Translation initiation factor eIF-2B subunit epsilon, N-terminal / MIF4G-like domain superfamily / Trimeric LpxA-like superfamily / Nucleotidyl transferase domain / W2 domain / Hexapeptide repeat / Initiation factor 2B-related / NagB/RpiA transferase-like / Methylthioribose-1-phosphate isomerase, N-terminal ...Armadillo-type fold / Translation initiation factor eIF-2B subunit epsilon, N-terminal / MIF4G-like domain superfamily / Trimeric LpxA-like superfamily / Nucleotidyl transferase domain / W2 domain / Hexapeptide repeat / Initiation factor 2B-related / NagB/RpiA transferase-like / Methylthioribose-1-phosphate isomerase, N-terminal / Bacterial transferase hexapeptide (six repeats) / Nucleotidyl transferase / Initiation factor 2 subunit family / eIF4-gamma/eIF5/eIF2-epsilon / W2 domain profile. / Nucleotide-diphospho-sugar transferases
Probable translation initiation factor eIF-2B subunit epsilon / Probable translation initiation factor eIF-2B subunit gamma / Probable translation initiation factor eIF-2B subunit delta / Translation initiation factor eIF-2B subunit alpha / Probable translation initiation factor eIF-2B subunit beta
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å
AuthorsKashiwagi, K. / Ito, T. / Yokoyama, S.
CitationJournal: Nature / Year: 2016
Title: Crystal structure of eukaryotic translation initiation factor 2B
Authors: Kashiwagi, K. / Takahashi, M. / Nishimoto, M. / Hiyama, T.B. / Higo, T. / Umehara, T. / Sakamoto, K. / Ito, T. / Yokoyama, S.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 27, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jun 21, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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: Probable translation initiation factor eIF-2B subunit beta
D: Probable translation initiation factor eIF-2B subunit beta
E: Probable translation initiation factor eIF-2B subunit gamma
F: Probable translation initiation factor eIF-2B subunit gamma
G: Probable translation initiation factor eIF-2B subunit delta
H: Probable translation initiation factor eIF-2B subunit delta
I: Probable translation initiation factor eIF-2B subunit epsilon
J: Probable translation initiation factor eIF-2B subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,52019
Polymers520,66610
Non-polymers8559
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43360 Å2
ΔGint-301 kcal/mol
Surface area142050 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)144.495, 209.234, 223.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Probable translation initiation factor eIF-2B subunit ... , 4 types, 8 molecules CDEFGHIJ

#2: Protein/peptide Probable translation initiation factor eIF-2B subunit beta / eIF-2B GDP-GTP exchange factor subunit beta


Mass: 43897.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tif222, SPAC343.14c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UT76
#3: Protein/peptide Probable translation initiation factor eIF-2B subunit gamma / eIF-2B GDP-GTP exchange factor subunit gamma


Mass: 50551.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tif223, SPAC4D7.09 / Production host: Escherichia coli (E. coli) / References: UniProt: P56288
#4: Protein/peptide Probable translation initiation factor eIF-2B subunit delta / eIF-2B GDP-GTP exchange factor subunit delta


Mass: 51652.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tif224, SPAC21E11.06 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09924
#5: Protein/peptide Probable translation initiation factor eIF-2B subunit epsilon / eIF-2B GDP-GTP exchange factor subunit epsilon


Mass: 76413.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tif225, SPAC8C9.15c / Production host: Escherichia coli (E. coli) / References: UniProt: P56287

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Protein/peptide / Non-polymers , 2 types, 11 molecules AB

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


Mass: 37817.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tif221, SPCC11E10.07c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9USP0
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4 / Phosphate

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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: 3.24 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG200MME, sodium chloride, Na/K phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→49.29 Å / Num. obs: 136112 / % possible obs: 99.6 % / Redundancy: 6.3 % / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.994→49.29 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 6808 5 %
Rwork0.2223 129253 -
Obs0.2247 136061 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.51 Å2 / Biso mean: 86.4482 Å2 / Biso min: 26.21 Å2
Refinement stepCycle: final / Resolution: 2.994→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28539 0 45 0 28584
Biso mean--86.54 --
Num. residues----3652
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.00729080
f_angle_d1.4439405
f_chiral_restr0.0834616
f_plane_restr0.0065032
f_dihedral_angle_d15.2410773
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9935-3.02750.42131950.40843885408090
3.0275-3.06310.43482240.37542324456100
3.0631-3.10050.41842300.371342864516100
3.1005-3.13970.38082250.352243034528100
3.1397-3.1810.33882320.30642254457100
3.181-3.22460.34612370.304142754512100
3.2246-3.27060.3212440.28742584502100
3.2706-3.31950.35772130.289143224535100
3.3195-3.37130.35662130.291942794492100
3.3713-3.42660.36162070.287343274534100
3.4266-3.48560.34782210.274142984519100
3.4856-3.5490.3432190.263943094528100
3.549-3.61730.31562310.249442774508100
3.6173-3.69110.27392350.245242984533100
3.6911-3.77130.2952310.233442614492100
3.7713-3.8590.27442540.218643054559100
3.859-3.95550.29032280.222442794507100
3.9555-4.06240.28922300.21843294559100
4.0624-4.18180.24532230.200743264549100
4.1818-4.31670.21872160.193843024518100
4.3167-4.47090.20062160.188443564572100
4.4709-4.64980.23172190.182943474566100
4.6498-4.86120.24332380.182543164554100
4.8612-5.11730.22452280.195843424570100
5.1173-5.43750.2792270.206843414568100
5.4375-5.85670.28092030.223643984601100
5.8567-6.4450.27362410.227243614602100
6.445-7.37490.32430.21544004643100
7.3749-9.28150.20292290.169844464675100
9.2815-49.29840.22192560.18754570482699

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