[English] 日本語
Yorodumi
- EMDB-72909: VPS13A central bridge domain -

+
Open data


ID or keywords:

Loading...

-
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


sperm mitochondrion organization / brain-derived neurotrophic factor receptor signaling pathway / neuronal dense core vesicle lumen / lysosomal protein catabolic process / protein retention in Golgi apparatus / response to environmental enrichment / microglia differentiation / neuroinflammatory response / Golgi to endosome transport / mitochondria-associated endoplasmic reticulum membrane contact site ...sperm mitochondrion organization / brain-derived neurotrophic factor receptor signaling pathway / neuronal dense core vesicle lumen / lysosomal protein catabolic process / protein retention in Golgi apparatus / response to environmental enrichment / microglia differentiation / neuroinflammatory response / Golgi to endosome transport / mitochondria-associated endoplasmic reticulum membrane contact site / neuron projection arborization / protein targeting to vacuole / neuromuscular process controlling balance / motor behavior / long-term synaptic depression / exploration behavior / cellular response to osmotic stress / lipid transport / flagellated sperm motility / protein secretion / social behavior / multicellular organism growth / adult locomotory behavior / lipid droplet / erythrocyte differentiation / mitochondrial membrane / gene expression / autophagy / intracellular protein localization / sperm midpiece / mitochondrial outer membrane / endosome membrane / neuron projection / 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-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72909.png

Downloads & links

-
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
Brightness
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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 °

-
Supplemental data

-
Half map: #1

Fileemd_72909_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72909_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : VPS13A/Calmodulin-XKR1 complex

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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more