9Y4B | pdb_00009y4b

Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta subunit (active-like-state) bound to the viral effector AcP10

PDB DOI: https://doi.org/10.2210/pdb9Y4B/pdb
EM Map EMD-72477: EMDB EMDataResource

Classification: TRANSLATION
Organism(s): Homo sapiens, Beluga whale coronavirus SW1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-02 Released: 2026-06-24
Deposition Author(s): Dalwadi, U., Croll, T., Subramanian, A., Lee, D.J., Arthur, C., Walter, P., Frost, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Allosteric Disordering of eIF2B Regulates the Integrated Stress Response

Dalwadi, U., Croll, T., Subramanian, A., Lee, D.J., Arthur, C., Walter, P., Frost, A.

To be published.

Macromolecule Content

Total Structure Weight: 571.33 kDa
Atom Count: 32,179
Modeled Residue Count: 4,116
Deposited Residue Count: 5,132
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit epsilon	A, B	721	Homo sapiens	Mutation(s): 0 Gene Names: EIF2B5, EIF2BE
UniProt & NIH Common Fund Data Resources
Find proteins for Q13144 (Homo sapiens) Explore Q13144 Go to UniProtKB: Q13144
PHAROS: Q13144 GTEx: ENSG00000145191
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13144
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF2B subunit beta	C, D	355	Homo sapiens	Mutation(s): 0 Gene Names: EIF2B2, EIF2BB
UniProt & NIH Common Fund Data Resources
Find proteins for P49770 (Homo sapiens) Explore P49770 Go to UniProtKB: P49770
PHAROS: P49770 GTEx: ENSG00000119718
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49770
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit delta	E, F	523	Homo sapiens	Mutation(s): 0 Gene Names: EIF2B4, EIF2BD
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI10 (Homo sapiens) Explore Q9UI10 Go to UniProtKB: Q9UI10
PHAROS: Q9UI10 GTEx: ENSG00000115211
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UI10
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit alpha	G, H	305	Homo sapiens	Mutation(s): 0 Gene Names: EIF2B1, EIF2BA
UniProt & NIH Common Fund Data Resources
Find proteins for Q14232 (Homo sapiens) Explore Q14232 Go to UniProtKB: Q14232
PHAROS: Q14232 GTEx: ENSG00000111361
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14232
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit gamma	I, J	452	Homo sapiens	Mutation(s): 0 Gene Names: EIF2B3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR50 (Homo sapiens) Explore Q9NR50 Go to UniProtKB: Q9NR50
PHAROS: Q9NR50 GTEx: ENSG00000070785
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NR50
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine kinase P10	K, L	210	Beluga whale coronavirus SW1	Mutation(s): 0 Gene Names: ORF10 EC: 2.7.1.48
UniProt
Find proteins for B2BW43 (Beluga whale coronavirus (strain SW1)) Explore B2BW43 Go to UniProtKB: B2BW43
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2BW43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain V [auth K] SDF format, chain W [auth L] SDF format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain V [auth K] MOL2 format, chain W [auth L] MOL2 format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain V [auth K] mmCIF format, chain W [auth L] mmCIF format, chain O [auth D]	N [auth C], O [auth D], V [auth K], W [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth C] Focus chain O [auth D] Focus chain V [auth K] Focus chain W [auth L] Interactions & Density Focus chain N [auth C] Focus chain O [auth D] Focus chain V [auth K] Focus chain W [auth L]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain U [auth F] MOL2 format, chain P [auth E] MOL2 format, chain U [auth F] mmCIF format, chain P [auth E] mmCIF format, chain U [auth F]	P [auth E], U [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P [auth E] Focus chain U [auth F] Interactions & Density Focus chain P [auth E] Focus chain U [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain Q [auth E] MOL2 format, chain M [auth B] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth E] mmCIF format, chain M [auth B] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth E]	M [auth B], Q [auth E], R [auth E], S [auth F], T [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain M [auth B] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F]