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- PDB-9yr6: Structure of HTTQ23-HAP40 complex bound to a small molecule ligand -

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Basic information

Entry
Database: PDB / ID: 9yr6
TitleStructure of HTTQ23-HAP40 complex bound to a small molecule ligand
Components
  • 40-kDa huntingtin-associated protein
  • Huntingtin
KeywordsPEPTIDE BINDING PROTEIN / Huntingtin / Polyglutamine expansion / small molecule ligand / ligand discovery
Function / homology
Function and homology information


vesicle cytoskeletal trafficking / : / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / negative regulation of proteasomal protein catabolic process / positive regulation of mitophagy / regulation of CAMKK-AMPK signaling cascade / profilin binding / positive regulation of cilium assembly ...vesicle cytoskeletal trafficking / : / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / negative regulation of proteasomal protein catabolic process / positive regulation of mitophagy / regulation of CAMKK-AMPK signaling cascade / profilin binding / positive regulation of cilium assembly / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / vesicle transport along microtubule / positive regulation of aggrephagy / positive regulation of lipophagy / Golgi organization / dynein intermediate chain binding / dynactin binding / phosphoprotein phosphatase activity / establishment of mitotic spindle orientation / Regulation of MECP2 expression and activity / postsynaptic cytosol / beta-tubulin binding / presynaptic cytosol / heat shock protein binding / inclusion body / centriole / autophagosome / cytoplasmic vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / kinase binding / p53 binding / late endosome / transmembrane transporter binding / early endosome / nuclear body / positive regulation of apoptotic process / axon / apoptotic process / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Factor VIII intron 22 protein / Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 ...Factor VIII intron 22 protein / Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
: / 40-kDa huntingtin-associated protein / Huntingtin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsBalakrishnan, S. / Deme, J. / Lea, S.M. / Harding, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Biorxiv / Year: 2025
Title: Identification and Characterization of a Small Molecule Ligand for the Huntingtin-HAP40 Complex
Authors: Balakrishnan, S. / Deme, J. / Lea, S.M. / Harding, R.J.
History
DepositionOct 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Huntingtin
B: 40-kDa huntingtin-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,1283
Polymers390,8152
Non-polymers3131
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Huntingtin / Huntington disease protein / HD protein


Mass: 349472.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTT, HD, IT15 / Production host: unidentified baculovirus / References: UniProt: P42858
#2: Protein 40-kDa huntingtin-associated protein / HAP40 / CpG island protein / Factor VIII intron 22 protein


Mass: 41342.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8A1, F8A2, F8A3 / Production host: unidentified baculovirus / References: UniProt: P23610
#3: Chemical ChemComp-A1CYY / 2-[(1R)-2,2-difluorocyclopropyl]-N-[(1-methyl-1H-indazol-6-yl)methyl]aniline


Mass: 313.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17F2N3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1HTT Q23 - HAP40 complex with small molecule ligandCOMPLEX#1-#20MULTIPLE SOURCES
2HTT-HAP40COMPLEX#1-#21RECOMBINANT
3Small molecule XS837367COMPLEXall1NATURALChemically synthesised
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.4 MDaNO
210.391 MDaNO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21unidentified baculovirus10469
32unidentified baculovirus10469
43unidentified baculovirus10469
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2150 mMSodium chlorideNaCl1
30.025 %w/vCHAPSC8H18N2O4S1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 51.1 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X

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Processing

EM software
IDNameVersionCategory
1SIMPLE3.1particle selection
2EPUimage acquisition
4SIMPLE3.1CTF correction
7Cootmodel fitting
9UCSF ChimeraXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1549562
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 387879 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6X90

6x90


Pdb chain-ID: A / Accession code: 6X90 / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421744
ELECTRON MICROSCOPYf_angle_d0.46929532
ELECTRON MICROSCOPYf_dihedral_angle_d23.8992935
ELECTRON MICROSCOPYf_chiral_restr0.0363508
ELECTRON MICROSCOPYf_plane_restr0.0033736

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