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- PDB-6k71: eIF2 - eIF2B complex -

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Basic information

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


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 / guanyl-nucleotide exchange factor complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex ...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 / guanyl-nucleotide exchange factor complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex / cytoplasmic translational initiation / translation factor activity, RNA binding / astrocyte differentiation / PERK-mediated unfolded protein response / negative regulation of guanyl-nucleotide exchange factor activity / astrocyte development / eukaryotic 48S preinitiation complex / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / regulation of translational initiation / myelination / oligodendrocyte development / positive regulation of translational initiation / nucleotidyltransferase activity / stress granule assembly / response to lithium ion / polysome / translation initiation factor binding / cellular response to amino acid starvation / ovarian follicle development / guanyl-nucleotide exchange factor activity / response to endoplasmic reticulum stress / translation initiation factor activity / central nervous system development / response to peptide hormone / translational initiation / positive regulation of translational fidelity / response to glucose / hippocampus development / cellular response to UV / cytoplasmic stress granule / ribosome binding / positive regulation of neuron death / regulation of translation / male gonad development / cellular response to heat / transmembrane transport / cellular response to oxidative stress / response to heat / T cell receptor signaling pathway / in utero embryonic development / aging / cadherin binding / GTPase activity / mRNA binding / protein autophosphorylation / synapse / 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
Trimeric LpxA-like superfamily / RNA-binding domain, S1 / S1 domain / Translation initiation factor IF2/IF5 / Translation initiation factor 2, alpha subunit / Nucleic acid-binding, OB-fold / Translation initiation factor 2, gamma subunit, C-terminal / Translation elongation factor EFTu-like, domain 2 / MIF4G-like domain superfamily / Hexapeptide repeat ...Trimeric LpxA-like superfamily / RNA-binding domain, S1 / S1 domain / Translation initiation factor IF2/IF5 / Translation initiation factor 2, alpha subunit / Nucleic acid-binding, OB-fold / Translation initiation factor 2, gamma subunit, C-terminal / Translation elongation factor EFTu-like, domain 2 / MIF4G-like domain superfamily / Hexapeptide repeat / Translation protein, beta-barrel domain superfamily / Armadillo-type fold / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / W2 domain / Translation initiation factor 2, alpha subunit, middle domain superfamily / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Nucleotidyl transferase domain / Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor 2, alpha subunit, C-terminal / NagB/RpiA transferase-like / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Transcription factor, GTP-binding domain / Nucleotide-diphospho-sugar transferases / P-loop containing nucleoside triphosphate hydrolase
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 support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
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
History
DepositionJun 5, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 10, 2019ID: 6JLW
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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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 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 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 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 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 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 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 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 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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