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- PDB-6o9z: Electron cryo-microscopy of the eukaryotic translation initiation... -

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Basic information

Entry
Database: PDB / ID: 6o9z
TitleElectron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to eukaryotic translation initiation factor 2 from Homo sapiens
Components
  • (Translation initiation factor eIF-2B subunit ...) x 5
  • Eukaryotic translation initiation factor 2 subunit 1
KeywordsTRANSLATION / eukaryotic translation initiation factor 2B / eukaryotic translation initiation factor 2
Function / homology
Function and homology information


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 / guanyl-nucleotide exchange factor complex / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex / cytoplasmic translational initiation ...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 / guanyl-nucleotide exchange factor complex / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex / cytoplasmic translational initiation / astrocyte differentiation / PERK-mediated unfolded protein response / negative regulation of guanyl-nucleotide exchange factor activity / astrocyte development / eukaryotic 48S preinitiation complex / regulation of translational initiation / myelination / oligodendrocyte development / positive regulation of translational initiation / stress granule assembly / nucleotidyltransferase activity / polysome / response to lithium ion / translation initiation factor binding / cellular response to amino acid starvation / translation initiation factor activity / guanyl-nucleotide exchange factor activity / ovarian follicle development / response to endoplasmic reticulum stress / central nervous system development / translational initiation / 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 heat / cellular response to oxidative stress / response to heat / T cell receptor signaling pathway / aging / protein autophosphorylation / synapse / positive regulation of apoptotic process / GTP binding / RNA binding / extracellular exosome / membrane / ATP binding / identical protein binding / plasma membrane / nucleus / cytosol / cytoplasm
RNA-binding domain, S1 / eIF4-gamma/eIF5/eIF2-epsilon / S1 domain / W2 domain / Translation initiation factor 2, alpha subunit, middle domain superfamily / Nucleotidyl transferase domain / Trimeric LpxA-like superfamily / Bacterial transferase hexapeptide (six repeats) / Translation initiation factor 2, alpha subunit / Hexapeptide repeat ...RNA-binding domain, S1 / eIF4-gamma/eIF5/eIF2-epsilon / S1 domain / W2 domain / Translation initiation factor 2, alpha subunit, middle domain superfamily / Nucleotidyl transferase domain / Trimeric LpxA-like superfamily / Bacterial transferase hexapeptide (six repeats) / Translation initiation factor 2, alpha subunit / Hexapeptide repeat / Nucleic acid-binding, OB-fold / MIF4G-like domain superfamily / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Translation initiation factor eIF-2B subunit alpha, N-terminal / NagB/RpiA transferase-like / Initiation factor 2 subunit family / Nucleotidyl transferase / S1 RNA binding domain / Eukaryotic translation initiation factor 2 alpha subunit / Armadillo-type fold / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Nucleotide-diphospho-sugar transferases / Translation initiation factor 2, alpha subunit, C-terminal / Translation initiation factor 2; subunit 1; domain 2 / Nucleic acid-binding proteins / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Translation initiation factor eIF-2B subunit gamma / Translation initiation factor eIF-2B subunit delta / Translation initiation factor eIF-2B subunit alpha / Translation initiation factor eIF-2B subunit epsilon / Translation initiation factor eIF-2B subunit beta / Eukaryotic translation initiation factor 2 subunit 1
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsNguyen, H.C. / Kenner, L.R. / Frost, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)55108523 United 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
History
DepositionMar 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: 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 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
M: Eukaryotic translation initiation factor 2 subunit 1


Theoretical massNumber of molelcules
Total (without water)600,79612
Polymers600,79612
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 Translation initiation factor eIF-2B subunit epsilon / eIF-2B GDP-GTP exchange factor subunit epsilon


Mass: 80452.586 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 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 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 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 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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Protein , 1 types, 2 molecules LM

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


Mass: 37238.121 Da / Num. of mol.: 2
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

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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 Alpha-P bound to eIF2B / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1,2,3,4,5,6 / 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: dev_3354: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34014 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01225572
ELECTRON MICROSCOPYf_angle_d1.14934804
ELECTRON MICROSCOPYf_dihedral_angle_d5.63815372
ELECTRON MICROSCOPYf_chiral_restr0.0654318
ELECTRON MICROSCOPYf_plane_restr0.0084460

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