9EMC | pdb_00009emc

RUVBL1/2 in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb9EMC/pdb
EM Map EMD-19817: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-11 Released: 2024-05-15
Deposition Author(s): Lopez-Perrote, A., Llorca, O., Garcia-Martin, C.
Funding Organization(s): Agencia Estatal de Investigacion (AEI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.26 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Mechanism of allosteric inhibition of RUVBL1-RUVBL2 by the small-molecule CB-6644

Garcia-Martin, C., Lopez-Perrote, A., Boskovic, J., Llorca, O.

(2024) Cell Rep Phys Sci

DOI: https://doi.org/10.1016/j.xcrp.2024.101982

Macromolecule Content

Total Structure Weight: 314.07 kDa
Atom Count: 15,489
Modeled Residue Count: 1,977
Deposited Residue Count: 2,820
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 1	A, C [auth B], D [auth C]	459	Homo sapiens	Mutation(s): 0 Gene Names: RUVBL1, INO80H, NMP238, TIP49, TIP49A EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y265 (Homo sapiens) Explore Q9Y265 Go to UniProtKB: Q9Y265
PHAROS: Q9Y265 GTEx: ENSG00000175792
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y265
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 2	B [auth D], E [auth F], F [auth E]	481	Homo sapiens	Mutation(s): 0 Gene Names: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y230 (Homo sapiens) Explore Q9Y230 Go to UniProtKB: Q9Y230
PHAROS: Q9Y230 GTEx: ENSG00000183207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y230
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain O [auth F] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth D] SDF format, chain G [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth F] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth D] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth F] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth D] mmCIF format, chain G [auth A]	G [auth A] I [auth D] K [auth B] M [auth C] O [auth F] G [auth A], I [auth D], K [auth B], M [auth C], O [auth F], Q [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain I [auth D] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth F] Focus chain Q [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth D] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth F] Focus chain Q [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain P [auth F] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth D] SDF format, chain H [auth A] MOL2 format, chain R [auth E] MOL2 format, chain P [auth F] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth D] MOL2 format, chain H [auth A] mmCIF format, chain R [auth E] mmCIF format, chain P [auth F] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth D] mmCIF format, chain H [auth A]	H [auth A] J [auth D] L [auth B] N [auth C] P [auth F] H [auth A], J [auth D], L [auth B], N [auth C], P [auth F], R [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth D] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth F] Focus chain R [auth E] Interactions & Density Focus chain H [auth A] Focus chain J [auth D] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth F] Focus chain R [auth E]