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- EMDB-9841: eIF2(aP) - eIF2B complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9841
TitleeIF2(aP) - eIF2B complex
Map data
SampleeIF2(aP) - eIF2B
  • eIF2B
  • eIF2(aP)
  • (Translation initiation factor eIF-2B subunit ...) x 5
  • (Eukaryotic translation initiation factor 2 subunit ...) x 2
  • eIF2b
Function / homology
Function and homology information


PERK regulates gene expression / L13a-mediated translational silencing of Ceruloplasmin expression / ABC-family proteins mediated transport / Recycling of eIF2:GDP / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / translation initiation ternary complex / glial limiting end-foot ...PERK regulates gene expression / L13a-mediated translational silencing of Ceruloplasmin expression / ABC-family proteins mediated transport / Recycling of eIF2:GDP / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / 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 / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex / astrocyte differentiation / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / PERK-mediated unfolded protein response / negative regulation of guanyl-nucleotide exchange factor activity / formation of translation preinitiation complex / astrocyte development / regulation of translational initiation / myelination / oligodendrocyte development / stress granule assembly / positive regulation of translational initiation / nucleotidyltransferase activity / translational initiation / translation initiation factor binding / response to lithium ion / polysome / guanyl-nucleotide exchange factor activity / ovarian follicle development / cellular response to amino acid starvation / translation initiation factor activity / response to endoplasmic reticulum stress / central nervous system development / response to peptide hormone / response to glucose / hippocampus development / cellular response to UV / cytoplasmic stress granule / transmembrane transport / positive regulation of neuron death / ribosome binding / regulation of translation / cellular response to oxidative stress / cellular response to heat / response to heat / T cell receptor signaling pathway / cadherin binding / aging / GTPase activity / synapse / protein autophosphorylation / positive regulation of apoptotic process / GTP binding / RNA binding / extracellular exosome / membrane / ATP binding / identical protein binding / plasma membrane / nucleus / cytosol / cytoplasm
Translational (tr)-type guanine nucleotide-binding (G) domain profile. / MIF4G-like domain superfamily / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Nucleotide-diphospho-sugar transferases / P-loop containing nucleoside triphosphate hydrolase / Translation initiation factor 2, alpha subunit, C-terminal / Translation initiation factor 2, alpha subunit, middle domain superfamily / RNA-binding domain, S1 / Armadillo-type fold ...Translational (tr)-type guanine nucleotide-binding (G) domain profile. / MIF4G-like domain superfamily / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Nucleotide-diphospho-sugar transferases / P-loop containing nucleoside triphosphate hydrolase / Translation initiation factor 2, alpha subunit, C-terminal / Translation initiation factor 2, alpha subunit, middle domain superfamily / RNA-binding domain, S1 / Armadillo-type fold / Translation initiation factor 2, gamma subunit, C-terminal / Nucleic acid-binding, OB-fold / Translation initiation factor 2, alpha subunit / Trimeric LpxA-like superfamily / Initiation factor 2B-related / Transcription factor, GTP-binding domain / Hexapeptide repeat / S1 domain / W2 domain / Translation elongation factor EFTu-like, domain 2 / Nucleotidyl transferase domain / Elongation factor Tu GTP binding domain / NagB/RpiA transferase-like / Translation protein, beta-barrel domain superfamily / eIF4-gamma/eIF5/eIF2-epsilon / W2 domain profile. / S1 domain profile. / Initiation factor eIF2 gamma, C terminal / Eukaryotic translation initiation factor 2 alpha subunit / Elongation factor Tu domain 2 / Initiation factor 2 subunit family / S1 RNA binding domain / Bacterial transferase hexapeptide (six repeats) / Nucleotidyl transferase
Eukaryotic translation initiation factor 2 subunit 1 / 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
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 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.
Validation ReportPDB-ID: 6jlx

SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2019 / Header (metadata) release: May 1, 2019 / Map release: May 1, 2019 / Update: May 15, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6jlx
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9841.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: 0.0104 / Movie #1: 0.018
Minimum - Maximum-0.05230381 - 0.07943972
Average (Standard dev.)0.000003626556 (±0.002943248)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0520.0790.000

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Supplemental data

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Sample components

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Entire eIF2(aP) - eIF2B

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

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Component #1: protein, eIF2(aP) - eIF2B

ProteinName: eIF2(aP) - eIF2B / 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(aP)

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

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Component #4: protein, Translation initiation factor eIF-2B subunit alpha

ProteinName: Translation initiation factor eIF-2B subunit alpha / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 33.754148 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Translation initiation factor eIF-2B subunit beta

ProteinName: Translation initiation factor eIF-2B subunit beta / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 39.039547 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Translation initiation factor eIF-2B subunit gamma

ProteinName: Translation initiation factor eIF-2B subunit gamma / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 50.30423 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Translation initiation factor eIF-2B subunit delta

ProteinName: Translation initiation factor eIF-2B subunit delta / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 57.640168 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Translation initiation factor eIF-2B subunit epsilon

ProteinName: Translation initiation factor eIF-2B subunit epsilon / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 80.466609 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, Eukaryotic translation initiation factor 2 subunit 1

ProteinName: Eukaryotic translation initiation factor 2 subunit 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 36.16118 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, eIF2b

ProteinName: eIF2b / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.016338 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, Eukaryotic translation initiation factor 2 subunit 3

ProteinName: Eukaryotic translation initiation factor 2 subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.178406 kDa
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: 719877
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

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