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- EMDB-73345: Consensus map of full-length human VPS13C in complex with calmodulin -

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Basic information

Entry
Database: EMDB / ID: EMD-73345
TitleConsensus map of full-length human VPS13C in complex with calmodulin
Map dataVPS13C consensus map
Sample
  • Complex: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
    • Complex: VPS13C
    • Complex: Calmodulin
KeywordsLipid transport protein / BLTP / lysosome membrane damage repair / membrane homeostasis / LIPID TRANSPORT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLi D / Reinisch KM
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73345.png

Downloads & links

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Map

FileDownload / File: emd_73345.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVPS13C consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 384 pix.
= 546.816 Å		1.42 Å/pix.
x 384 pix.
= 546.816 Å		1.42 Å/pix.
x 384 pix.
= 546.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.424 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-2.5231605 - 3.7124019
Average (Standard dev.)-0.00017347954 (±0.024350954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 546.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73345_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: original, unsharpened VPS13C consensus map

Fileemd_73345_additional_1.map
Annotationoriginal, unsharpened VPS13C consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of VPS13C consensus map; flipped

Fileemd_73345_half_map_1.map
AnnotationHalf map A of VPS13C consensus map; flipped
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of VPS13C consensus map

Fileemd_73345_half_map_2.map
AnnotationHalf map B of VPS13C consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.

EntireName: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
Components
  • Complex: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
    • Complex: VPS13C
    • Complex: Calmodulin

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Supramolecule #1: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.

SupramoleculeName: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
type: complex / ID: 1 / Parent: 0
Details: The 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.

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Supramolecule #2: VPS13C

SupramoleculeName: VPS13C / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Calmodulin

SupramoleculeName: Calmodulin / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.04 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 392473
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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