9PMW | pdb_00009pmw

Structure of HTTQ23-HAP40 complex bound to macrocycles HHL1, HD4 and HL2

• PDB DOI: https://doi.org/10.2210/pdb9PMW/pdb
• EM Map EMD-71743: EMDB EMDataResource

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): Yes 


• Deposited: 2025-07-18 Released: 2025-08-20 
• 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: 2.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

High-Affinity, Structure-Validated and Selective Macrocyclic Peptide Tools for Chemical Biology Studies of Huntingtin.

Wolf, E., Fanti, R., Ikenoue, T., Deme, J.C., Balakrishnan, S., Keith, B.A., Alteen, M.G., Chandrasekaran, R., Yadav, M., Bhajiawala, R., Ackloo, S., Feng, J., Pouladi, M.A., Edwards, A.M., Wilson, D., Lea, S.M., Suga, H., Harding, R.J.

(2025) bioRxiv 

• PubMed: 41030958 
• DOI: https://doi.org/10.1101/2025.08.06.668955
• Primary Citation of Related Structures:  
  9PMW, 9PN0


• PubMed Abstract: 
  

  Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion in the Huntingtin ( HTT ) gene, with no disease-modifying therapies currently available. The precise molecular function of the HTT protein is unclear, and the lack of selective chemical tools has limited functional studies. We have identified and characterized macrocyclic peptide binders targeting HTT. These binders exhibit low-nanomolar affinity in vitro and engage distinct HTT and HTT-HAP40 interfaces, as revealed by hydrogen-deuterium exchange mass spectrometry and cryo-electron microscopy. Chemoproteomics confirmed selective binding in cell extracts from wildtype but not HTT-null cell lines. HAP40 consistently and stoichiometrically co-purified with HTT across cell lines, including with HTT variants containing different CAG repeat lengths, highlighting the broad presence of the HTT-HAP40 complex.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G1L7, Canada.
Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Djavad Mowafaghian Centre for Brain Health, Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.
Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada.
Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto ON M5S 3M2, Canada.
Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 396.81 kDa 
• Atom Count: 21,388 
• Modeled Residue Count: 2,733 
• Deposited Residue Count: 3,600 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HHL1	A [auth C]	19	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HD4	B [auth D]	19	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HL2	C [auth E]	17	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Huntingtin	D [auth A]	3,156	Homo sapiens	Mutation(s): 2  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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40-kDa huntingtin-associated protein	E [auth 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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.10 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: 2025-08-20 
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: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2025-10-15
  Changes: Data collection, Database references