[English] 日本語
Yorodumi
- PDB-5b04: Crystal structure of the eukaryotic translation initiation factor... -

+
Open data


ID or keywords:

Loading...

-
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 / eukaryotic translation initiation factor 2B complex / cytoplasmic translational initiation / guanyl-nucleotide exchange factor complex / translation initiation factor binding / translational initiation / negative regulation of TORC1 signaling / translation initiation factor activity / guanyl-nucleotide exchange factor activity / cytosol
Similarity search - Function
Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain ...Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / 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. / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases / Armadillo-type fold
Similarity search - Domain/homology
PHOSPHATE ION / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit gamma / Translation initiation factor eIF2B subunit delta / Translation initiation factor eIF2B subunit alpha / Translation initiation factor eIF2B subunit beta
Similarity search - Component
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.
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
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43360 Å2
ΔGint-301 kcal/mol
Surface area142050 Å2
MethodPISA
Unit cell
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

-
Components

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

#2: Protein 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 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 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 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

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

#1: Protein 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 / Phosphate


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729080
X-RAY DIFFRACTIONf_angle_d1.4439405
X-RAY DIFFRACTIONf_chiral_restr0.0834616
X-RAY DIFFRACTIONf_plane_restr0.0065032
X-RAY DIFFRACTIONf_dihedral_angle_d15.2410773
LS refinement shell

Refine-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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more