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- EMDB-9842: eIF2 - eIF2B (2 molecule) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-9842
TitleeIF2 - eIF2B (2 molecule)
Map data
SampleeIF2 - eIF2B (2 molecule):
eIF2B / eIF2 / eIF2Ba / eIF2Bb / eIF2Bg / eIF2Bd / eIF2Be / eIF2a / eIF2b / eIF2g
Function / homology
Function and homology information


male germ cell proliferation / translation initiation ternary complex / glial limiting end-foot / positive regulation of type B pancreatic cell apoptotic process / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / guanyl-nucleotide exchange factor complex / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / astrocyte development ...male germ cell proliferation / translation initiation ternary complex / glial limiting end-foot / positive regulation of type B pancreatic cell apoptotic process / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / guanyl-nucleotide exchange factor complex / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / astrocyte development / multi-eIF complex / cytoplasmic translational initiation / astrocyte differentiation / translation factor activity, RNA binding / negative regulation of guanyl-nucleotide exchange factor activity / PERK-mediated unfolded protein response / protein-synthesizing GTPase / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / myelination / regulation of translational initiation / oligodendrocyte development / positive regulation of translational initiation / stress granule assembly / nucleotidyltransferase activity / response to lithium ion / polysome / translation initiation factor binding / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / ovarian follicle development / response to endoplasmic reticulum stress / translational initiation / translation initiation factor activity / response to peptide hormone / central nervous system development / response to glucose / positive regulation of translational fidelity / hippocampus development / cellular response to UV / cytoplasmic stress granule / positive regulation of neuron death / male gonad development / ribosome binding / cellular response to heat / cellular response to oxidative stress / regulation of translation / transmembrane transport / response to heat / T cell receptor signaling pathway / in utero embryonic development / aging / cadherin binding / GTPase activity / protein autophosphorylation / mRNA binding / synapse / positive regulation of apoptotic process / GTP binding / RNA binding / extracellular exosome / membrane / ATP binding / identical protein binding / plasma membrane / metal ion binding / nucleus / cytosol / cytoplasm
Trimeric LpxA-like superfamily / W2 domain / S1 domain / Translation initiation factor 2, alpha subunit / Nucleic acid-binding, OB-fold / Initiation factor eIF2 gamma, C-terminal / Translation initiation factor IF2/IF5 / MIF4G-like domain superfamily / Armadillo-type fold / Hexapeptide repeat ...Trimeric LpxA-like superfamily / W2 domain / S1 domain / Translation initiation factor 2, alpha subunit / Nucleic acid-binding, OB-fold / Initiation factor eIF2 gamma, C-terminal / Translation initiation factor IF2/IF5 / MIF4G-like domain superfamily / Armadillo-type fold / Hexapeptide repeat / Translation initiation factor IF2/IF5, N-terminal / Translation elongation factor EFTu-like, domain 2 / Translation initiation factor IF2/IF5, zinc-binding / Translation protein, beta-barrel domain superfamily / RNA-binding domain, S1 / Translation initiation factor 2, alpha subunit, middle domain superfamily / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Nucleotidyl transferase domain / Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor 2, alpha subunit, C-terminal / NagB/RpiA transferase-like / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translational (tr)-type GTP-binding domain / Nucleotide-diphospho-sugar transferases / P-loop containing nucleoside triphosphate hydrolase / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal
Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit 3 / Translation initiation factor eIF-2B subunit beta / Translation initiation factor eIF-2B subunit epsilon / Translation initiation factor eIF-2B subunit alpha / Translation initiation factor eIF-2B subunit gamma / Translation initiation factor eIF-2B subunit delta
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsKashiwagi K / Yokoyama T / Ito T
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, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseMay 1, 2019-
UpdateJun 12, 2019-
Current statusJun 12, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0179
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0179
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9842.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 250 pix.
= 367.5 Å
1.47 Å/pix.
x 250 pix.
= 367.5 Å
1.47 Å/pix.
x 250 pix.
= 367.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.47 Å
Density
Contour LevelBy AUTHOR: 0.0179 / Movie #1: 0.0179
Minimum - Maximum-0.025003737 - 0.07427283
Average (Standard dev.)0.00019365162 (±0.0034214372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 367.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.471.471.47
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z367.500367.500367.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0250.0740.000

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Supplemental data

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Sample components

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Entire eIF2 - eIF2B (2 molecule)

EntireName: eIF2 - eIF2B (2 molecule) / Number of components: 11

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Component #1: protein, eIF2 - eIF2B (2 molecule)

ProteinName: eIF2 - eIF2B (2 molecule) / Recombinant expression: No

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Component #2: protein, eIF2B

ProteinName: eIF2B / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, eIF2

ProteinName: eIF2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, eIF2Ba

ProteinName: eIF2Ba / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, eIF2Bb

ProteinName: eIF2Bb / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, eIF2Bg

ProteinName: eIF2Bg / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, eIF2Bd

ProteinName: eIF2Bd / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, eIF2Be

ProteinName: eIF2Be / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, eIF2a

ProteinName: eIF2a / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, eIF2b

ProteinName: eIF2b / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, eIF2g

ProteinName: eIF2g / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 35184
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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