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- EMDB-0649: Electron cryo-microscopy of the eukaryotic translation initiation... -

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Basic information

Entry
Database: EMDB / ID: EMD-0649
TitleElectron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to translation initiation factor 2 from Homo sapiens
Map data
SampleeIF2B bound to eIF2
  • (Translation initiation factor eIF-2B subunit ...) x 5
  • (Eukaryotic translation initiation factor 2 subunit ...) x 2
  • Translation initiation factor eiF2 beta-subunit
  • ligand
Function / homology
Function and homology information


translation initiation ternary complex / glial limiting end-foot / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / positive regulation of type B pancreatic cell apoptotic process / guanyl-nucleotide exchange factor complex / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / translation factor activity, RNA binding / multi-eIF complex ...translation initiation ternary complex / glial limiting end-foot / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / positive regulation of type B pancreatic cell apoptotic process / guanyl-nucleotide exchange factor complex / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / translation factor activity, RNA binding / multi-eIF complex / astrocyte differentiation / cytoplasmic translational initiation / astrocyte development / PERK-mediated unfolded protein response / negative regulation of guanyl-nucleotide exchange factor activity / protein-synthesizing GTPase / eukaryotic 48S preinitiation complex / formation of translation preinitiation complex / regulation of translational initiation / myelination / oligodendrocyte development / positive regulation of translational initiation / stress granule assembly / response to lithium ion / translation initiation factor binding / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / ovarian follicle development / polysome / 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 / ribosome binding / cellular response to heat / regulation of translation / transmembrane transport / cellular response to oxidative stress / response to heat / T cell receptor signaling pathway / aging / cadherin binding / GTPase activity / protein autophosphorylation / positive regulation of apoptotic process / GTP binding / RNA binding / extracellular exosome / membrane / ATP binding / identical protein binding / plasma membrane / nucleus / cytosol / cytoplasm
Translation protein, beta-barrel domain superfamily / Initiation factor 2B-related / Nucleic acid-binding, OB-fold / Armadillo-type fold / RNA-binding domain, S1 / Translation elongation factor EFTu-like, domain 2 / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translational (tr)-type GTP-binding domain / Translation initiation factor 2, alpha subunit, C-terminal / Translation initiation factor 2, alpha subunit ...Translation protein, beta-barrel domain superfamily / Initiation factor 2B-related / Nucleic acid-binding, OB-fold / Armadillo-type fold / RNA-binding domain, S1 / Translation elongation factor EFTu-like, domain 2 / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translational (tr)-type GTP-binding domain / Translation initiation factor 2, alpha subunit, C-terminal / Translation initiation factor 2, alpha subunit / Trimeric LpxA-like superfamily / MobA-like NTP transferase / Initiation factor eIF2 gamma, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nucleotide-diphospho-sugar transferases / Translation initiation factor eIF-2B subunit epsilon, N-terminal / NagB/RpiA transferase-like / Hexapeptide repeat / Translation initiation factor eIF-2B subunit alpha, N-terminal / S1 domain / Initiation factor 2B-like, C-terminal / W2 domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / MIF4G-like domain superfamily
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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsNguyen H / Kenner L / Frost A
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 ReportSummary, Full report, XML, About validation report
History
DepositionMar 8, 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: 0.327
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.327
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o81
  • Surface level: 0.327
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0649.png

Downloads & links

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Map

FileDownload / File: emd_0649.map.gz / Format: CCP4 / Size: 476.8 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 500 pix.
= 411. Å		0.82 Å/pix.
x 500 pix.
= 411. Å		0.82 Å/pix.
x 500 pix.
= 411. 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.327 / Movie #1: 0.327
Minimum - Maximum-0.82193613 - 1.9078244
Average (Standard dev.)0.0003476412 (±0.058941033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 411.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z411.000411.000411.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.8221.9080.000

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Supplemental data

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Sample components

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Entire eIF2B bound to eIF2

EntireName: eIF2B bound to eIF2 / Number of components: 10

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Component #1: protein, eIF2B bound to eIF2

ProteinName: eIF2B bound to eIF2 / 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: 80.366531 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: 36.16118 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Eukaryotic translation initiation factor 2 subunit 3

ProteinName: Eukaryotic translation initiation factor 2 subunit 3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 51.150422 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, Translation initiation factor eiF2 beta-subunit

ProteinName: Translation initiation factor eiF2 beta-subunit / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.209482 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: ligand, 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)eth...

LigandName: 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.451343 kDa

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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: 11640
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

6o81

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