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- EMDB-0664: Electron cryo-microscopy of the eukaryotic translation initiation... -

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Basic information

Entry
Database: EMDB / ID: EMD-0664
TitleElectron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to eukaryotic translation initiation factor 2 from Homo sapiens
Map data
SampleeIF2 Alpha-P bound to eIF2B
  • (Translation initiation factor eIF-2B subunit ...) x 5
  • Eukaryotic translation initiation factor 2 subunit 1
Function / homology
Function and homology information


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 / multi-eIF complex / cytoplasmic translational initiation ...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 / multi-eIF complex / cytoplasmic translational initiation / astrocyte differentiation / PERK-mediated unfolded protein response / negative regulation of guanyl-nucleotide exchange factor activity / astrocyte development / eukaryotic 48S preinitiation complex / regulation of translational initiation / myelination / oligodendrocyte development / positive regulation of translational initiation / stress granule assembly / nucleotidyltransferase activity / polysome / response to lithium ion / translation initiation factor binding / cellular response to amino acid starvation / translation initiation factor activity / guanyl-nucleotide exchange factor activity / ovarian follicle development / response to endoplasmic reticulum stress / central nervous system development / translational initiation / response to peptide hormone / response to glucose / hippocampus development / cellular response to UV / cytoplasmic stress granule / ribosome binding / positive regulation of neuron death / regulation of translation / transmembrane transport / cellular response to heat / cellular response to oxidative stress / response to heat / T cell receptor signaling pathway / aging / protein autophosphorylation / synapse / positive regulation of apoptotic process / GTP binding / RNA binding / extracellular exosome / membrane / ATP binding / identical protein binding / plasma membrane / nucleus / cytosol / cytoplasm
Nucleic acid-binding, OB-fold / Nucleotidyl transferase domain / Translation initiation factor 2, alpha subunit / Trimeric LpxA-like superfamily / Initiation factor 2B-related / MIF4G-like domain superfamily / Armadillo-type fold / Hexapeptide repeat / RNA-binding domain, S1 / Translation initiation factor 2, alpha subunit, middle domain superfamily ...Nucleic acid-binding, OB-fold / Nucleotidyl transferase domain / Translation initiation factor 2, alpha subunit / Trimeric LpxA-like superfamily / Initiation factor 2B-related / MIF4G-like domain superfamily / Armadillo-type fold / Hexapeptide repeat / RNA-binding domain, S1 / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Nucleotide-diphospho-sugar transferases / Translation initiation factor eIF-2B subunit epsilon, N-terminal / NagB/RpiA transferase-like / Translation initiation factor eIF-2B subunit alpha, N-terminal / W2 domain / S1 domain / Initiation factor 2B-like, C-terminal
Eukaryotic translation initiation factor 2 subunit 1 / 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: 3.03 Å
AuthorsNguyen HC / Kenner LR / Frost AS
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)55108523 United States
CitationJournal: Science / Year: 2019
Title: eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response.
Authors: Lillian R Kenner / Aditya A Anand / Henry C Nguyen / Alexander G Myasnikov / Carolin J Klose / Lea A McGeever / Jordan C Tsai / Lakshmi E Miller-Vedam / Peter Walter / Adam Frost /
Abstract: The integrated stress response (ISR) tunes the rate of protein synthesis. Control is exerted by phosphorylation of the general translation initiation factor eIF2. eIF2 is a guanosine triphosphatase ...The integrated stress response (ISR) tunes the rate of protein synthesis. Control is exerted by phosphorylation of the general translation initiation factor eIF2. eIF2 is a guanosine triphosphatase that becomes activated by eIF2B, a two-fold symmetric and heterodecameric complex that functions as eIF2's dedicated nucleotide exchange factor. Phosphorylation converts eIF2 from a substrate into an inhibitor of eIF2B. We report cryo-electron microscopy structures of eIF2 bound to eIF2B in the dephosphorylated state. The structures reveal that the eIF2B decamer is a static platform upon which one or two flexible eIF2 trimers bind and align with eIF2B's bipartite catalytic centers to catalyze nucleotide exchange. Phosphorylation refolds eIF2α, allowing it to contact eIF2B at a different interface and, we surmise, thereby sequestering it into a nonproductive complex.
Validation ReportPDB-ID: 6o9z

SummaryFull reportAbout validation report
History
DepositionMar 15, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6o9z
  • Surface level: 3
  • 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_0664.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 352 pix.
= 289.344 Å
0.82 Å/pix.
x 352 pix.
= 289.344 Å
0.82 Å/pix.
x 352 pix.
= 289.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 1.9 / Movie #1: 3
Minimum - Maximum-8.685509 - 14.365423
Average (Standard dev.)-0.010631724 (±0.78712493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 289.344 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z289.344289.344289.344
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-8.68614.365-0.011

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Supplemental data

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Sample components

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Entire eIF2 Alpha-P bound to eIF2B

EntireName: eIF2 Alpha-P bound to eIF2B / Number of components: 7

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Component #1: cellular-component, eIF2 Alpha-P bound to eIF2B

Cellular-componentName: eIF2 Alpha-P bound to eIF2B / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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

ProteinName: Translation initiation factor eIF-2B subunit epsilon / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 80.452586 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Translation initiation factor eIF-2B subunit beta

ProteinName: Translation initiation factor eIF-2B subunit beta / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 41.008578 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: 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 #5: 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 #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, Eukaryotic translation initiation factor 2 subunit 1

ProteinName: Eukaryotic translation initiation factor 2 subunit 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 37.238121 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

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

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 80 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 / Number of projections: 34014
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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