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- PDB-6k71: eIF2 - eIF2B complex -

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Entry
Database: PDB / ID: 6k71
TitleeIF2 - eIF2B complex
Components
  • (Eukaryotic translation initiation factor 2 subunit ...) x 3
  • (Translation initiation factor eIF-2B subunit ...) x 5
KeywordsTRANSLATION / Translation Initiation
Function / homology
Function and homology information


ABC-family proteins mediated transport / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / PERK regulates gene expression / male germ cell proliferation / translation initiation ternary complex ...ABC-family proteins mediated transport / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / PERK regulates gene expression / male germ cell proliferation / 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 / astrocyte differentiation / multi-eIF complex / translation factor activity, RNA binding / PERK-mediated unfolded protein response / negative regulation of guanyl-nucleotide exchange factor activity / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / astrocyte development / formation of translation preinitiation complex / regulation of translational initiation / myelination / oligodendrocyte development / nucleotidyltransferase activity / stress granule assembly / positive regulation of translational initiation / response to lithium ion / guanyl-nucleotide exchange factor activity / translation initiation factor binding / translational initiation / polysome / cellular response to amino acid starvation / translation initiation factor activity / ovarian follicle development / 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 / ribosome binding / positive regulation of neuron death / regulation of translation / transmembrane transport / cellular response to oxidative stress / male gonad development / cellular response to heat / in utero embryonic development / response to heat / T cell receptor signaling pathway / aging / cadherin binding / GTPase activity / mRNA binding / synapse / protein autophosphorylation / positive regulation of apoptotic process / GTP binding / RNA binding / extracellular exosome / membrane / ATP binding / identical protein binding / plasma membrane / metal ion binding / nucleus / cytosol / cytoplasm
W2 domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5, N-terminal / Armadillo-type fold / MIF4G-like domain superfamily / Translation initiation factor 2, gamma subunit, C-terminal / Nucleic acid-binding, OB-fold / Translation initiation factor 2, alpha subunit / Trimeric LpxA-like superfamily ...W2 domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5, N-terminal / Armadillo-type fold / MIF4G-like domain superfamily / Translation initiation factor 2, gamma subunit, C-terminal / Nucleic acid-binding, OB-fold / Translation initiation factor 2, alpha subunit / Trimeric LpxA-like superfamily / Translation protein, beta-barrel domain superfamily / Translation initiation factor 2, alpha subunit, middle domain superfamily / Nucleotidyl transferase domain / Translation elongation factor EFTu-like, domain 2 / W2 domain / S1 domain / Translation initiation factor IF2/IF5 / Hexapeptide repeat / Transcription factor, GTP-binding domain / Initiation factor 2B-related / RNA-binding domain, S1 / Translation initiation factor 2, alpha subunit, C-terminal / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / S1 RNA binding domain / S1 domain profile. / Initiation factor eIF2 gamma, C terminal / Eukaryotic translation initiation factor 2 alpha subunit / Elongation factor Tu domain 2 / eIF4-gamma/eIF5/eIF2-epsilon / Domain found in IF2B/IF5 / Initiation factor 2 subunit family / P-loop containing nucleoside triphosphate hydrolase / Nucleotidyl transferase / Bacterial transferase hexapeptide (six repeats) / Elongation factor Tu GTP binding domain / NagB/RpiA transferase-like / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Nucleotide-diphospho-sugar transferases
Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit 2 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKashiwagi, K. / Yokoyama, T. / Ito, T.
Funding supportJapan , 2件
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJapan
Japan Agency for Medical Research and Development (AMED)Japan
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jun 5, 2019 / Release: Jul 10, 2019
RevisionDateData content typeProviderType
1.0Jul 10, 2019Structure modelrepositoryInitial release

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Assembly

Deposited unit
A: Translation initiation factor eIF-2B subunit alpha
B: Translation initiation factor eIF-2B subunit alpha
C: Translation initiation factor eIF-2B subunit beta
D: Translation initiation factor eIF-2B subunit beta
E: Translation initiation factor eIF-2B subunit gamma
F: Translation initiation factor eIF-2B subunit gamma
G: Translation initiation factor eIF-2B subunit delta
H: Translation initiation factor eIF-2B subunit delta
I: Translation initiation factor eIF-2B subunit epsilon
J: Translation initiation factor eIF-2B subunit epsilon
K: Eukaryotic translation initiation factor 2 subunit 1
M: Eukaryotic translation initiation factor 2 subunit 2
P: Eukaryotic translation initiation factor 2 subunit 3


Theoretical massNumber of molelcules
Total (without water)648,20313
Polymers648,20313
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area39430 Å2
ΔGint-180 kcal/mol
Surface area185970 Å2

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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 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
#2: Protein/peptide Translation initiation factor eIF-2B subunit beta / S20I15 / S20III15 / eIF-2B GDP-GTP exchange factor subunit beta


Mass: 39039.547 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 gamma / eIF2Bg / 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
#4: 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
#5: 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

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

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


Mass: 36161.180 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 2 / Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 38454.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2S2, EIF2B / Production host: Escherichia coli (E. coli) / References: UniProt: P20042
#8: 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

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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 - eIF2B complex / Type: COMPLEX / 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
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82123 / Symmetry type: POINT

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