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- PDB-6jly: eIF2a - eIF2B complex -

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Basic information

Entry
Database: PDB / ID: 6jly
TitleeIF2a - eIF2B complex
Components
  • (Probable translation initiation factor eIF-2B subunit ...) x 4
  • Eukaryotic translation initiation factor 2 subunit alpha
  • Translation initiation factor eIF-2B subunit alpha
KeywordsTRANSLATION / Translation Initiation
Function / homology
Function and homology information


Recycling of eIF2:GDP / Recycling of eIF2:GDP / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2B complex / eukaryotic translation initiation factor 2 complex / multi-eIF complex / cytoplasmic translational initiation / formation of translation preinitiation complex / guanyl-nucleotide exchange factor complex / eukaryotic 48S preinitiation complex ...Recycling of eIF2:GDP / Recycling of eIF2:GDP / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2B complex / eukaryotic translation initiation factor 2 complex / multi-eIF complex / cytoplasmic translational initiation / formation of translation preinitiation complex / guanyl-nucleotide exchange factor complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding / translational initiation / negative regulation of TORC1 signaling / translation initiation factor activity / guanyl-nucleotide exchange factor activity / cytoplasmic stress granule / ribosome binding / ribosome / RNA binding / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 2; subunit 1; domain 2 / 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 ...Translation initiation factor 2; subunit 1; domain 2 / 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. / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleotide-diphospho-sugar transferases / Nucleic acid-binding proteins / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Armadillo-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Eukaryotic translation initiation factor 2 subunit alpha / 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)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsKashiwagi, K. / Ito, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Science / Year: 2019
Title: Structural basis for eIF2B inhibition in integrated stress response.
Authors: Kazuhiro Kashiwagi / Takeshi Yokoyama / Madoka Nishimoto / Mari Takahashi / Ayako Sakamoto / Mayumi Yonemochi / Mikako Shirouzu / Takuhiro Ito /
Abstract: A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation ...A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Normally, unphosphorylated eIF2 transfers the methionylated initiator tRNA to the ribosome in a guanosine 5'-triphosphate-dependent manner. By contrast, phosphorylated eIF2 inhibits its specific guanine nucleotide exchange factor, eIF2B. To elucidate how the eIF2 phosphorylation status regulates the eIF2B activity, we determined cryo-electron microscopic and crystallographic structures of eIF2B in complex with unphosphorylated or phosphorylated eIF2. The unphosphorylated and phosphorylated forms of eIF2 bind to eIF2B in completely different manners: the nucleotide exchange-active and -inactive modes, respectively. These structures explain how phosphorylated eIF2 dominantly inhibits the nucleotide exchange activity of eIF2B.
History
DepositionMar 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 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

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
L: Eukaryotic translation initiation factor 2 subunit alpha
M: Eukaryotic translation initiation factor 2 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)590,95320
Polymers590,19312
Non-polymers7608
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44630 Å2
ΔGint-271 kcal/mol
Surface area167700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.563, 207.992, 155.595
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABLM

#1: Protein Translation initiation factor eIF-2B subunit alpha / eIF2Ba / 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: Protein Eukaryotic translation initiation factor 2 subunit alpha / eIF2a / eIF-2-alpha


Mass: 34763.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Escherichia coli (E. coli) / References: UniProt: P20459

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

#2: Protein Probable translation initiation factor eIF-2B subunit beta / eIF2Bb / 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 / eIF2Bg / 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 / eIF2Bd / 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 / eIF2Be / 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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Non-polymers , 1 types, 8 molecules

#7: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4

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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: 4.23 Å3/Da / Density % sol: 77.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium acetate, sodium citrate, PEG 4000, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 123415 / % possible obs: 99.6 % / Redundancy: 3.5 % / Net I/σ(I): 13
Reflection shellResolution: 3.5→3.71 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 3.5→49.314 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8
RfactorNum. reflection% reflection
Rfree0.2598 3869 1.62 %
Rwork0.2239 --
obs0.2245 123323 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→49.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31771 0 40 0 31811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432352
X-RAY DIFFRACTIONf_angle_d0.58743794
X-RAY DIFFRACTIONf_dihedral_angle_d3.21519710
X-RAY DIFFRACTIONf_chiral_restr0.0445102
X-RAY DIFFRACTIONf_plane_restr0.0045593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4963-3.53890.36391270.3537653X-RAY DIFFRACTION89
3.5389-3.58370.39691370.36248246X-RAY DIFFRACTION97
3.5837-3.63080.39211430.35498531X-RAY DIFFRACTION99
3.6308-3.68060.39721420.35468423X-RAY DIFFRACTION99
3.6806-3.73310.36671380.35068392X-RAY DIFFRACTION99
3.7331-3.78880.38721410.34318592X-RAY DIFFRACTION98
3.7888-3.8480.38231340.32558414X-RAY DIFFRACTION98
3.848-3.91110.35831410.3138432X-RAY DIFFRACTION98
3.9111-3.97850.39481420.29968466X-RAY DIFFRACTION98
3.9785-4.05080.36561340.28938397X-RAY DIFFRACTION97
4.0508-4.12870.34311350.27318161X-RAY DIFFRACTION96
4.1287-4.21290.30751470.2568425X-RAY DIFFRACTION98
4.2129-4.30440.32421420.24718487X-RAY DIFFRACTION98
4.3044-4.40450.26381410.23948410X-RAY DIFFRACTION97
4.4045-4.51460.22131310.20728305X-RAY DIFFRACTION98
4.5146-4.63660.24931420.2048523X-RAY DIFFRACTION99
4.6366-4.77290.21041340.18738465X-RAY DIFFRACTION98
4.7729-4.92680.23191460.198482X-RAY DIFFRACTION99
4.9268-5.10270.26491240.20558457X-RAY DIFFRACTION98
5.1027-5.30680.2471340.20888412X-RAY DIFFRACTION97
5.3068-5.5480.22351400.21588352X-RAY DIFFRACTION97
5.548-5.84010.24491330.22368400X-RAY DIFFRACTION98
5.8401-6.20530.32441470.23258441X-RAY DIFFRACTION99
6.2053-6.68340.28131430.2358526X-RAY DIFFRACTION99
6.6834-7.3540.25161370.22128465X-RAY DIFFRACTION98
7.354-8.41360.26151360.19668326X-RAY DIFFRACTION97
8.4136-10.58290.14451370.16018433X-RAY DIFFRACTION98
10.5829-49.31870.2171410.19138276X-RAY DIFFRACTION96

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