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- PDB-9y3v: Eukaryotic translation initiation factor 2-B (eIF2B) bound to the... -

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Basic information

Entry
Database: PDB / ID: 9y3v
TitleEukaryotic translation initiation factor 2-B (eIF2B) bound to the viral effector AcP10
Components
  • (Translation initiation factor eIF-2B subunit ...) x 4
  • Translation initiation factor eIF2B subunit alpha
  • Uridine kinase P10
KeywordsTRANSLATION / Guanine nucleotide exchange factor / GEF / initiation
Function / homology
Function and homology information


uridine/cytidine kinase / uridine kinase activity / eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / astrocyte development / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / positive regulation of translational initiation ...uridine/cytidine kinase / uridine kinase activity / eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / astrocyte development / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / positive regulation of translational initiation / response to glucose / ovarian follicle development / myelination / translation initiation factor activity / translation initiation factor binding / guanyl-nucleotide exchange factor activity / response to endoplasmic reticulum stress / central nervous system development / hippocampus development / translational initiation / response to peptide hormone / regulation of translation / T cell receptor signaling pathway / response to heat / host cell perinuclear region of cytoplasm / positive regulation of apoptotic process / GTP binding / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / 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 / : / : / : / : / : ...Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / 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. / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uridine kinase P10 / 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)
Beluga whale coronavirus SW1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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: To Be Published
Title: Allosteric Disordering of eIF2B Regulates the Integrated Stress Response
Authors: Dalwadi, U. / Croll, T. / Subramanian, A. / Lee, D.J. / Arthur, C. / Walter, P. / Frost, A.
History
DepositionSep 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 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
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 eIF2B subunit alpha
H: Translation initiation factor eIF2B subunit alpha
I: Translation initiation factor eIF-2B subunit gamma
J: Translation initiation factor eIF-2B subunit gamma
K: Uridine kinase P10
L: Uridine kinase P10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)574,15222
Polymers573,77912
Non-polymers37310
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Translation initiation factor eIF-2B subunit ... , 4 types, 8 molecules ABCDEFIJ

#1: 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
#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
#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 , 2 types, 4 molecules GHKL

#4: Protein Translation initiation factor eIF2B subunit alpha / eIF2B 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
#6: Protein Uridine kinase P10 / Accessory protein P10 / AcP10


Mass: 23715.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beluga whale coronavirus SW1 / Gene: ORF10 / Production host: Escherichia coli (E. coli) / References: UniProt: B2BW43, uridine/cytidine kinase

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Non-polymers , 4 types, 11 molecules

#7: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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
IDNameTypeEntity IDParent-IDSource
1Eukaryotic translation initiation factor 2B bound to AcP10COMPLEX#1-#60MULTIPLE SOURCES
2AcP10COMPLEX#61RECOMBINANT
3eIF2BCOMPLEX#1-#51RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.569120 MDaNO
2123681 kDa/nmNO
310.521758 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Beluga whale coronavirus SW1694015
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Details: 20 mM HEPES KOH pH 7.4, 200 mM KCl, 5 mM MgCl2, 1 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid or 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acidHEPES1
2200 mMPotassium ChlorideKCl1
35 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: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16068
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPUimage acquisition
4cryoSPARC4.4.1CTF correction
7ISOLDEmodel fitting
9cryoSPARC4.4.1initial Euler assignment
10cryoSPARC4.4.1final Euler assignment
11cryoSPARC4.4.1classification
12cryoSPARC4.4.13D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1805332
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220193 / Num. of class averages: 4 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeDetails (eV)Initial refinement model-IDSource nameType
17L7G

7l7g

7L7GeIF2B1PDBexperimental model
2AF-Q9HA47-F1AcP102AlphaFoldin silico model

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