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- PDB-9pmw: Structure of HTTQ23-HAP40 complex bound to macrocycles HHL1, HD4 ... -

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Basic information

Entry
Database: PDB / ID: 9pmw
TitleStructure of HTTQ23-HAP40 complex bound to macrocycles HHL1, HD4 and HL2
Components
  • 40-kDa huntingtin-associated protein
  • HD4
  • HHL1
  • HL2
  • Huntingtin
KeywordsPEPTIDE BINDING PROTEIN / Huntingtin / Macrocycles / Polyglutamine expansion
Function / homology
Function and homology information


vesicle cytoskeletal trafficking / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / 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 inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / 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 / establishment of mitotic spindle orientation / dynactin binding / phosphoprotein phosphatase activity / Regulation of MECP2 expression and activity / postsynaptic cytosol / beta-tubulin binding / presynaptic cytosol / inclusion body / heat shock protein binding / 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)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 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: High-Affinity, Structure-Validated and Selective Macrocyclic Peptide Tools for Chemical Biology Studies of Huntingtin
Authors: 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. / ...Authors: 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.
History
DepositionJul 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HHL1
D: HD4
E: HL2
A: Huntingtin
B: 40-kDa huntingtin-associated protein


Theoretical massNumber of molelcules
Total (without water)396,8155
Polymers396,8155
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide HHL1


Mass: 2131.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Macrocycle peptide / Source: (synth.) synthetic construct (others)
#2: Protein/peptide HD4


Mass: 2024.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide HL2


Mass: 1830.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein Huntingtin / Huntington disease protein / HD protein


Mass: 349486.375 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
#5: 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
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 macrocycles HHL1, HD4 and HL2COMPLEX#5, #1-#40MULTIPLE SOURCES
2HTT-HAP40COMPLEX#5, #41RECOMBINANT
3Macrocyclic peptidesCOMPLEX#1-#31NATURALChemically 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: 51.8 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: 988456
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 230039 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6X90

6x90


Pdb chain-ID: A / Accession code: 6X90 / Source name: PDB / Type: experimental model

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