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- PDB-6o85: Electron cryo-microscopy of the eukaryotic translation initiation... -

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Entry
Database: PDB / ID: 6o85
TitleElectron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to eukaryotic translation initiation factor 2 from Homo sapiens
Components
  • (Eukaryotic translation initiation factor 2 subunit ...) x 3
  • (Translation initiation factor eIF-2B subunit ...) x 5
KeywordsTRANSLATION / eukaryotic translation initiation factor 2B / eukaryotic translation initiation factor 2
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
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsNguyen, H.C. / Kenner, L.R. / Frost, A.S.
Funding supportUnited States , 1件
OrganizationGrant numberCountry
Howard Hughes Medical Institute55108523United 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 Report
SummaryFull reportAbout validation report
DateDeposition: Mar 8, 2019 / Release: May 15, 2019Array

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Structure visualization

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Assembly

Deposited unit
A: Translation initiation factor eIF-2B subunit epsilon
B: Translation initiation factor eIF-2B subunit epsilon
C: Translation initiation factor eIF-2B subunit beta
D: Translation initiation factor eIF-2B subunit beta
E: Translation initiation factor eIF-2B subunit delta
F: Translation initiation factor eIF-2B subunit delta
G: Translation initiation factor eIF-2B subunit alpha
H: Translation initiation factor eIF-2B subunit alpha
I: Translation initiation factor eIF-2B subunit gamma
J: Translation initiation factor eIF-2B subunit gamma
L: Eukaryotic translation initiation factor 2 subunit 1
S: Eukaryotic translation initiation factor 2 subunit 3
d: Eukaryotic translation initiation factor 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)615,21714
Polymers614,76513
Non-polymers4511
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Translation initiation factor eIF-2B subunit ... , 5 types, 10 molecules ABCDEFGHIJ

#1: Protein/peptide Translation initiation factor eIF-2B subunit epsilon / eIF-2B GDP-GTP exchange factor subunit epsilon


Mass: 80466.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B5, EIF2BE / Production host: Escherichia coli (E. coli) / References: UniProt: Q13144
#2: Protein/peptide Translation initiation factor eIF-2B subunit beta / S20I15 / S20III15 / eIF-2B GDP-GTP exchange factor subunit beta


Mass: 41008.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B2, EIF2BB / Production host: Escherichia coli (E. coli) / References: UniProt: P49770
#3: Protein/peptide Translation initiation factor eIF-2B subunit delta / eIF-2B GDP-GTP exchange factor subunit delta


Mass: 57640.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B4, EIF2BD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI10
#4: Protein/peptide Translation initiation factor eIF-2B subunit alpha / eIF-2B GDP-GTP exchange factor subunit alpha


Mass: 33754.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B1, EIF2BA / Production host: Escherichia coli (E. coli) / References: UniProt: Q14232
#5: Protein/peptide Translation initiation factor eIF-2B subunit gamma / eIF-2B GDP-GTP exchange factor subunit gamma


Mass: 50304.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR50

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Eukaryotic translation initiation factor 2 subunit ... , 3 types, 3 molecules LSd

#6: Protein/peptide Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


Mass: 36029.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2S1, EIF2A / Production host: Escherichia coli (E. coli) / References: UniProt: P05198
#7: Protein/peptide Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 51178.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2S3, EIF2G / Production host: Escherichia coli (E. coli) / References: UniProt: P41091
#8: Protein/peptide Eukaryotic translation initiation factor 2 subunit beta


Mass: 1209.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 1 molecules

#9: Chemical ChemComp-C7B / 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 451.343 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H24Cl2N2O4 / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2S3, EIF2G / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: eIF2 bound to eIF2B / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44157 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00354687
f_angle_d0.80297795
f_dihedral_angle_d8.29922215
f_chiral_restr0.0674863
f_plane_restr0.0058965

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