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- PDB-8yao: Cryo-ET structure of huntingtin actin dimer complex -

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Basic information

Entry
Database: PDB / ID: 8yao
TitleCryo-ET structure of huntingtin actin dimer complex
Components
  • Actin, alpha skeletal muscle
  • Huntingtin
KeywordsCYTOSOLIC PROTEIN/CONTRACTILE PROTEIN / Huntington's disease / cytoskeleton / CYTOSOLIC PROTEIN / CYTOSOLIC PROTEIN-CONTRACTILE PROTEIN complex
Function / homology
Function and homology information


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 / 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 inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / 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 / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / Golgi organization / troponin I binding / filamentous actin / mesenchyme migration / dynein intermediate chain binding / establishment of mitotic spindle orientation / dynactin binding / actin filament bundle assembly / phosphoprotein phosphatase activity / skeletal muscle myofibril / striated muscle thin filament / Regulation of MECP2 expression and activity / skeletal muscle thin filament assembly / actin monomer binding / postsynaptic cytosol / beta-tubulin binding / presynaptic cytosol / skeletal muscle fiber development / stress fiber / titin binding / inclusion body / heat shock protein binding / actin filament polymerization / centriole / autophagosome / cytoplasmic vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway / actin filament / filopodium / protein destabilization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinase binding / calcium-dependent protein binding / p53 binding / late endosome / lamellipodium / cell body / transmembrane transporter binding / early endosome / hydrolase activity / positive regulation of apoptotic process / axon / protein domain specific binding / apoptotic process / dendrite / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT ...Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Huntingtin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 20.8 Å
AuthorsSong, J.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Cryo-ET Structure of Huntingtin and Actin complex
Authors: Song, J.J.
History
DepositionFeb 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 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

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Assembly

Deposited unit
A: Huntingtin
N: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
K: Actin, alpha skeletal muscle
L: Actin, alpha skeletal muscle
M: Actin, alpha skeletal muscle
a: Huntingtin
n: Actin, alpha skeletal muscle
b: Actin, alpha skeletal muscle
c: Actin, alpha skeletal muscle
d: Actin, alpha skeletal muscle
e: Actin, alpha skeletal muscle
f: Actin, alpha skeletal muscle
g: Actin, alpha skeletal muscle
h: Actin, alpha skeletal muscle
i: Actin, alpha skeletal muscle
j: Actin, alpha skeletal muscle
k: Actin, alpha skeletal muscle
l: Actin, alpha skeletal muscle
m: Actin, alpha skeletal muscle


Theoretical massNumber of molelcules
Total (without water)1,784,68428
Polymers1,784,68428
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 Huntingtin / Huntington disease protein / HD protein


Mass: 348128.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTT, HD, IT15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P42858
#2: Protein ...
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Huntingtin-Actin complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 6000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 170 e/Å2 / Avg electron dose per subtomogram: 2.79 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 20.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21000 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 42 / Num. of volumes extracted: 84019
Atomic model buildingProtocol: RIGID BODY FIT

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