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- PDB-9yqq: Cryo-EM structure of the VPS13C C-terminal region -

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Basic information

Entry
Database: PDB / ID: 9yqq
TitleCryo-EM structure of the VPS13C C-terminal region
ComponentsIntermembrane lipid transfer protein VPS13C
KeywordsLIPID TRANSPORT / Lipid transport protein / BLTP / membrane repair / membrane homeostasis / VPS13C
Function / homology
Function and homology information


dense core granule membrane / negative regulation of type 2 mitophagy / protein retention in Golgi apparatus / Golgi to endosome transport / protein targeting to vacuole / lipid transport / lipid droplet / mitochondrion organization / response to insulin / late endosome ...dense core granule membrane / negative regulation of type 2 mitophagy / protein retention in Golgi apparatus / Golgi to endosome transport / protein targeting to vacuole / lipid transport / lipid droplet / mitochondrion organization / response to insulin / late endosome / late endosome membrane / mitochondrial outer membrane / lysosome / lysosomal membrane / endoplasmic reticulum membrane / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain / Vacuolar protein sorting-associated protein 13 / Vacuolar protein sorting-associated protein 13-like, N-terminal domain / : / : / VPS13-like family middle region / Vacuolar-sorting associated protein 13, adaptor binding domain / Intermembrane lipid transfer protein VPS13, C-terminal / VPS13-like family N-terminal region
Similarity search - Domain/homology
Intermembrane lipid transfer protein VPS13C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi, D. / Reinisch, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Aligning Science Across Parkinsons (ASAP)ASAP-000580 United States
CitationJournal: bioRxiv / Year: 2025
Title: Insights into the regulation of VPS13 family bridge-like lipid transfer proteins from the structure of VPS13C.
Authors: Dazhi Li / Xinbo Wang / Bodan Hu / Hongyan Hao / Stephanie Hamill / Yuting Li / Guochao Chen / Pietro De Camilli / Karin M Reinisch /
Abstract: Bridge-like lipid transfer proteins (BLTPs) play central roles in redistributing lipids from their primary site of synthesis in the endoplasmic reticulum to other organelles. They comprise bridge- ...Bridge-like lipid transfer proteins (BLTPs) play central roles in redistributing lipids from their primary site of synthesis in the endoplasmic reticulum to other organelles. They comprise bridge-domains spanning between organelles at contact sites that allow lipids to transit the cytosol between adjacent membranes. The assembly of BLTPs into complexes with adaptor proteins enables their lipid transfer ability. To address the mechanisms underlying assembly and regulation of BLTP complexes, we used cryo-EM to resolve the structure of one such BLTP, the Parkinson's protein VPS13C, at near-atomic resolution. The structure identifies a lipid-transfer-nonpermissive conformation, where the built-in C-terminal VAB adaptor module blocks the end of the lipid transfer bridge, interfering with lipid delivery. We also identify calmodulin, central to calcium signaling, as a VPS13 partner, suggesting calcium regulation of VPS13 function. Altogether, this structure of intact VPS13C serves as starting point to understand its regulation and, more broadly, that of other BLTPs.
History
DepositionOct 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intermembrane lipid transfer protein VPS13C


Theoretical massNumber of molelcules
Total (without water)425,8751
Polymers425,8751
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 Intermembrane lipid transfer protein VPS13C / Vacuolar protein sorting-associated protein 13C


Mass: 425875.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS13C, KIAA1421 / Production host: Homo sapiens (human) / References: UniProt: Q709C8
Has protein modificationN

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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
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.COMPLEXThe plasmid encoding full-length VPS13C with a C-terminal 3xFLAG tag was transfected into Expi293F cells. The VPS13C was transiently expressed. Endogenous calmodulin was co-purified with VPS13C.all0MULTIPLE SOURCES
2VPS13CCOMPLEXall1RECOMBINANT
3CalmodulinCOMPLEX1NATURAL
Molecular weightValue: 0.442 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
SpecimenConc.: 0.04 mg/ml / Embedding 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: 2500 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionDetails: PathCTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 403001 / Symmetry type: POINT

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