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- EMDB-0651: Electron cryo-microscopy of the eukaryotic translation initiation... -

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Basic information

Entry
Database: EMDB / ID: EMD-0651
TitleElectron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to eukaryotic translation initiation factor 2 from Homo sapiens
Map data
SampleeIF2 bound to eIF2B
  • (Translation initiation factor eIF-2B subunit ...) x 5
  • (Eukaryotic translation initiation factor 2 subunit ...) x 3
  • ligand
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: 3.03 Å
AuthorsNguyen HC / Kenner LR / Frost AS
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: 6o85

SummaryFull reportAbout validation report
DateDeposition: Mar 8, 2019 / Header (metadata) release: May 15, 2019 / Map release: May 15, 2019 / Update: May 15, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6o85
  • Surface level: 0.4
  • 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_0651.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 394.56 Å
0.82 Å/pix.
x 480 pix.
= 394.56 Å
0.82 Å/pix.
x 480 pix.
= 394.56 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: 0.4 / Movie #1: 0.4
Minimum - Maximum-1.1773602 - 2.372217
Average (Standard dev.)-0.000057249665 (±0.067027055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z394.560394.560394.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-1.1772.372-0.000

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Supplemental data

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Sample components

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Entire eIF2 bound to eIF2B

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

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

Cellular-componentName: eIF2 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: 80.466609 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: 1 / Recombinant expression: No
MassTheoretical: 36.029984 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: 1 / Recombinant expression: No
MassTheoretical: 51.178406 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 beta

ProteinName: Eukaryotic translation initiation factor 2 subunit beta
Number of Copies: 1 / 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
SourceSpecies: 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
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: 44157
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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