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- PDB-9y5r: Eukaryotic translation initiation factor 2-B (eIF2B) bound to pho... -

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Basic information

Entry
Database: PDB / ID: 9y5r
TitleEukaryotic translation initiation factor 2-B (eIF2B) bound to phosphorylated eIF2alpha (NTD)
Components
  • (Translation initiation factor eIF-2B subunit ...) x 5
  • Eukaryotic translation initiation factor 2 subunit 1
KeywordsTRANSLATION / Guanine nucleotide exchange factor / GEF / initiation
Function / homology
Function and homology information


translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / response to manganese-induced endoplasmic reticulum stress / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / HRI-mediated signaling / eukaryotic translation initiation factor 2B complex / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of translational initiation in response to stress ...translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / response to manganese-induced endoplasmic reticulum stress / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / HRI-mediated signaling / eukaryotic translation initiation factor 2B complex / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / Recycling of eIF2:GDP / PERK regulates gene expression / response to kainic acid / eukaryotic translation initiation factor 2 complex / regulation of translational initiation in response to stress / astrocyte development / eukaryotic 48S preinitiation complex / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of translational initiation / Response of EIF2AK4 (GCN2) to amino acid deficiency / response to glucose / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / ovarian follicle development / mitophagy / myelination / translation initiation factor activity / translation initiation factor binding / guanyl-nucleotide exchange factor activity / response to endoplasmic reticulum stress / cellular response to amino acid starvation / stress granule assembly / central nervous system development / hippocampus development / translational initiation / PKR-mediated signaling / response to peptide hormone / ABC-family protein mediated transport / cytoplasmic stress granule / cellular response to UV / regulation of translation / T cell receptor signaling pathway / cellular response to heat / response to heat / ribosome binding / cellular response to oxidative stress / positive regulation of apoptotic process / synapse / GTP binding / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related ...Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Trimeric LpxA-like superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / Nucleotide-diphospho-sugar transferases / S1 RNA binding domain / S1 domain / Armadillo-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2 subunit 1 / Translation initiation factor eIF2B subunit beta / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit alpha / Translation initiation factor eIF2B subunit gamma / Translation initiation factor eIF2B subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsDalwadi, U. / Croll, T. / Subramanian, A. / Lee, D.J. / Arthur, C. / Walter, P. / Frost, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: Allosteric disordering of eIF2B regulates the integrated stress response
Authors: Dalwadi, U. / Subramanian, A. / Deal, A. / Conrad, J.E. / Nadjsombati, T. / Venkatesh, M. / Boone, M. / Egea, P.F. / He, L. / Jain, N. / Lee, D.J. / Liu, Y. / Reineke, L.C. / Saito, K. / ...Authors: Dalwadi, U. / Subramanian, A. / Deal, A. / Conrad, J.E. / Nadjsombati, T. / Venkatesh, M. / Boone, M. / Egea, P.F. / He, L. / Jain, N. / Lee, D.J. / Liu, Y. / Reineke, L.C. / Saito, K. / Talledge, N. / Toutkoushian, H. / Le Vasseur, M. / Zappa, F. / de Groot, R.J. / Acosta-Alvear, D. / Arthur, C.P. / Nunnari, J. / Marqusee, S. / Lawrence, R.E. / Costa-Mattioli, M. / Crawford, J.J. / van Kuppeveld, F.J.M. / Croll, T.I. / Walter, P. / Frost, A.
History
DepositionSep 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)577,81516
Polymers577,61412
Non-polymers2024
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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-2-alpha / eIF-2A / eIF-2alpha / eIF2-alpha


Mass: 25647.111 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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Non-polymers , 2 types, 4 molecules

#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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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: eIF2B bound to phospho-eIF2alpha(S51P) / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 577213.2 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Details: 40 mM HEPES KOH pH 7.4, 150 mM KCl, 2 mM MgCl2, 1 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
140 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMPotassium chlorideKCl1
32 mMMagnesium ChlorideMgCl21
41 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 16000 nm / Nominal defocus min: 6000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16195
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
4cryoSPARC4.2.1CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
13ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 221364
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130953 / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6o9z

6o9z


Accession code: 6o9z / Source name: PDB / Type: experimental model
RefinementResolution: 3.01→3.01 Å / Num. reflection obs: 3921563 / Average fsc work: 0.7403
Displacement parametersBiso mean: 102.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0079321560.0119
ELECTRON MICROSCOPYs_angle_nonh_deg1.6375435441.8265
ELECTRON MICROSCOPYs_dihedral_angle_1_deg7.476140105
ELECTRON MICROSCOPYs_dihedral_angle_2_deg4.087710125
ELECTRON MICROSCOPYs_dihedral_angle_3_deg11.1953867810
ELECTRON MICROSCOPYs_dihedral_angle_6_deg14.3204160810
ELECTRON MICROSCOPYs_chiral_restr0.065450640.1311
ELECTRON MICROSCOPYs_planes0.0051446960.02
ELECTRON MICROSCOPYs_nbd0.2105431300.2
ELECTRON MICROSCOPYs_nbtor0.2242574660.2
ELECTRON MICROSCOPYs_hbond_nbd0.10476580.2
ELECTRON MICROSCOPYs_metal_ion0.208220.2

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