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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: To Be Published
Title: Insights into the regulation of VPS13 family bridge-like lipid transfer proteins from the structure of VPS13C.
Authors: Li D / Wang X / Hu B / Hao H / De Camilli P / Reinisch K
History
DepositionOct 15, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 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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