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- PDB-6jlw: eIF2 - eIF2B complex -

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Entry
Database: PDB / ID: 6jlw
TitleeIF2 - eIF2B complex
Components
  • (Eukaryotic translation initiation factor 2 subunit ...) x 2
  • (Translation initiation factor eIF-2B subunit ...) x 5
  • eIF2b
KeywordsTRANSLATION / Translation Initiation
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: 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: Mar 7, 2019 / Release: May 1, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 1, 2019Structure modelrepositoryInitial release
1.1May 15, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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: eIF2b
P: Eukaryotic translation initiation factor 2 subunit 3


Theoretical massNumber of molelcules
Total (without water)611,76513
Polymers611,76513
Non-polymers00
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 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 ... , 2 types, 2 molecules KP

#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: Homo sapiens (human) / References: UniProt: P05198
#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: Homo sapiens (human) / References: UniProt: P41091

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Protein/peptide , 1 types, 1 molecules M

#7: Protein/peptide eIF2b /


Mass: 2016.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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

Component

Source: RECOMBINANT / Type: COMPLEX

IDNameEntity IDParent-ID
1eIF2 - eIF2B1, 2, 3, 4, 5, 6, 7, 80
2eIF2B1,2,3,4,51
3eIF26,7,81
Source (natural)

Ncbi tax-ID: 9606 / Organism: Homo sapiens (human)

IDEntity assembly-ID
12
23
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Homo sapiens (human)9606
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

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
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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