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- EMDB-72909: VPS13A central bridge domain -

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Basic information

Entry
Database: EMDB / ID: EMD-72909
TitleVPS13A central bridge domain
Map data
Sample
  • Complex: VPS13A/Calmodulin-XKR1 complex
    • Protein or peptide: Intermembrane lipid transfer protein VPS13A
KeywordsVPS13A / BLTP / RBG motif / LIPID TRANSPORT
Function / homology
Function and homology information


neuronal dense core vesicle lumen / protein retention in Golgi apparatus / lysosomal protein catabolic process / Golgi to endosome transport / protein targeting to vacuole / mitochondria-associated endoplasmic reticulum membrane contact site / lipid transport / sperm midpiece / lipid droplet / autophagy ...neuronal dense core vesicle lumen / protein retention in Golgi apparatus / lysosomal protein catabolic process / Golgi to endosome transport / protein targeting to vacuole / mitochondria-associated endoplasmic reticulum membrane contact site / lipid transport / sperm midpiece / lipid droplet / autophagy / intracellular protein localization / mitochondrial membrane / mitochondrial outer membrane / neuron projection / endosome membrane / lysosomal membrane / neuronal cell body / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / 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 VPS13A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsHu B / Reinisch KM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131715 United States
CitationJournal: Cell / Year: 2026
Title: Mechanism of lipid transfer by bridge-like protein VPS13A and the scramblase XK.
Authors: Bodan Hu / Daniel Álvarez / Cristian Rocha-Roa / Valentin Guyard / Dazhi Li / Yara Ahmed / Xinbo Wang / Pietro De Camilli / Stefano Vanni / Karin M Reinisch /
Abstract: In eukaryotes, bridge-like lipid-transfer proteins (BLTPs) are central in mediating vesicle-independent lipid transfer between organelles. BLTPs span the cytosolic space between organelles at contact ...In eukaryotes, bridge-like lipid-transfer proteins (BLTPs) are central in mediating vesicle-independent lipid transfer between organelles. BLTPs span the cytosolic space between organelles at contact sites, featuring hydrophobic channels for lipids to travel between membranes. How BLTPs cooperate with partner proteins to orchestrate lipid delivery remains a mystery. Here, we used cryo-electron microscopy to visualize a complex comprising the prototypical BLTP VPS13A and the plasma membrane-localized scramblase XK at near-atomic resolution. VPS13A interacts with XK via its pleckstrin homology domain, priming VPS13A's bridge-like lipid-transfer domain to deliver lipids directly to the cytosolic leaflet of the acceptor membrane. In molecular dynamics simulations, this arrangement allows for robust lipid transfer. Newly delivered lipids can then be equilibrated between leaflets of the membrane bilayer by the scramblase, allowing for membrane growth. Mechanistic insights regarding lipid delivery by VPS13A are directly applicable to all VPS13 proteins and, more broadly, to all BLTP family members.
History
DepositionSep 27, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72909.png

Downloads & links

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Map

FileDownload / File: emd_72909.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 672 pix.
= 559.104 Å		0.83 Å/pix.
x 672 pix.
= 559.104 Å		0.83 Å/pix.
x 672 pix.
= 559.104 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.0
Minimum - Maximum-39.146023 - 104.421524000000005
Average (Standard dev.)0.00000000000078 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 559.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72909_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72909_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : VPS13A/Calmodulin-XKR1 complex

EntireName: VPS13A/Calmodulin-XKR1 complex
Components
  • Complex: VPS13A/Calmodulin-XKR1 complex
    • Protein or peptide: Intermembrane lipid transfer protein VPS13A

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Supramolecule #1: VPS13A/Calmodulin-XKR1 complex

SupramoleculeName: VPS13A/Calmodulin-XKR1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Intermembrane lipid transfer protein VPS13A

MacromoleculeName: Intermembrane lipid transfer protein VPS13A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.476547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VNMTTFKIRF EVPKVLIEFY HLVGDCELSV VEILVLGLGA EIEIRTYDLK ANAFLKEFCL KCPEYLDENK KPVYLVTTLD NTMEDLLTL EYVKAEKNVP DLKSTYNNVL QLIKVNFSSL DIHLHTEALL NTINYLHNIL PQSEEKSAPV STTETEDKGD V IKKLALKL ...String:
VNMTTFKIRF EVPKVLIEFY HLVGDCELSV VEILVLGLGA EIEIRTYDLK ANAFLKEFCL KCPEYLDENK KPVYLVTTLD NTMEDLLTL EYVKAEKNVP DLKSTYNNVL QLIKVNFSSL DIHLHTEALL NTINYLHNIL PQSEEKSAPV STTETEDKGD V IKKLALKL STNEDIITLQ ILAELSCLQI FIQDQKCNIS EIKIEGLDSE MIMRPSETEI NAKLRNIIVL DSDITAIYKK AV YITGKEV FSFKMVSYMD ATAGSAYTDM NVVDIQVNLI VGCIEVVFVT KFLYSILAFI DNFQAAKQAL AEATVQAAGM AAT GVKELA QRSSRMALDI NIKAPVVVIP QSPVSENVFV ADFGLITMTN TFHMITESQS SPPPVIDLIT IKLSEMRLYR SRFI NDAYQ EVLDLLLPLN LEVVVERNLC WEWYQEVPCF NVNAQLKPME FILSQEDITT IFKTLHGNIW YEKDGSASPA VTKDQ YSAT SGVTTNASHH SGGATVVTAA VVEVHSRALL VKTTLNISFK TDDLTMVLYS PGPKQASFTD VRDPSLKLAE FKLENI IST LKMYTDGSTF SSFSLKNCIL DDKRPHVKKA TPRMIGLTVG FDKKDMMDIK YRKVRDGCVT DAVFQEMYIC ASVEFLQ TV ANVFLEAYTT GTAV

UniProtKB: Intermembrane lipid transfer protein VPS13A

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.2) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 464055
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
FSC plot (resolution estimation)

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