9YR6 | pdb_00009yr6

Structure of HTTQ23-HAP40 complex bound to a small molecule ligand

• PDB DOI: https://doi.org/10.2210/pdb9YR6/pdb
• EM Map EMD-73361: EMDB EMDataResource

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2025-10-16 Released: 2025-12-03 
• Deposition Author(s): Balakrishnan, S., Deme, J., Lea, S.M., Harding, R.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Identification and Characterization of a Small Molecule Ligand for the Huntingtin-HAP40 Complex

Balakrishnan, S., Deme, J., Lea, S.M., Harding, R.J.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.11.21.689733v1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 391.13 kDa 
• Atom Count: 21,208 
• Modeled Residue Count: 2,709 
• Deposited Residue Count: 3,545 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Huntingtin	A	3,156	Homo sapiens	Mutation(s): 0  Gene Names: HTT, HD, IT15
UniProt & NIH Common Fund Data Resources
Find proteins for P42858 (Homo sapiens) Explore P42858  Go to UniProtKB:  P42858
PHAROS:  P42858 GTEx:  ENSG00000197386

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
40-kDa huntingtin-associated protein	B	389	Homo sapiens	Mutation(s): 0  Gene Names: F8A1, F8A2, F8A3
UniProt & NIH Common Fund Data Resources
Find proteins for P23610 (Homo sapiens) Explore P23610  Go to UniProtKB:  P23610
GTEx:  ENSG00000277150

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CYY (Subject of Investigation/LOI)	C [auth A]	2-[(1R)-2,2-difluorocyclopropyl]-N-[(1-methyl-1H-indazol-6-yl)methyl]aniline C18 H17 F2 N3 XFVSAPGKSJEWES-OAHLLOKOSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	UCSF ChimeraX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Balakrishnan, S., Deme, J., Lea, S.M., Harding, R.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release