9EMA | pdb_00009ema

RUVBL1/2 in complex with ATP and CB-6644 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9EMA/pdb
• EM Map EMD-19815: EMDB EMDataResource

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


• Deposited: 2024-03-07 Released: 2024-05-15 
• Deposition Author(s): Lopez-Perrote, A., Llorca, O., Garcia-Martin, C.
• Funding Organization(s): Agencia Estatal de Investigacion (AEI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C6  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 315.74 kDa 
• Atom Count: 15,562 
• Modeled Residue Count: 1,974 
• Deposited Residue Count: 2,820 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 1	A, B, 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 2	D, E, F	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H5V (Subject of Investigation/LOI)	H [auth A], J [auth B], L [auth C]	5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide C29 H34 Cl F N4 O5 VYCOZEBCSAQCES-UHFFFAOYSA-N
ATP	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], R [auth F]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	N [auth D], P [auth E], Q [auth F], S [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	ISOLDE	1.7
MODEL REFINEMENT	PHENIX	1.20.1-4487
MODEL REFINEMENT	Coot	0.9.8.5

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Lopez-Perrote, A., Llorca, O., Garcia-Martin, C.

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Funding Organization	Location	Grant Number
Agencia Estatal de Investigacion (AEI)	Spain	PID2020-114429RB-I00

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release
  
• Version 2.0: 2025-03-12
  Changes: Advisory, Data collection, Database references, Polymer sequence, Source and taxonomy, Structure summary