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- PDB-9yg5: VPS13A/Ct-XKR1 -

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Basic information

Entry
Database: PDB / ID: 9yg5
TitleVPS13A/Ct-XKR1
Components
  • Endoplasmic reticulum membrane adapter protein XK
  • Intermembrane lipid transfer protein VPS13A
KeywordsLIPID TRANSPORT / VPS13A / XKR1 / BLTPs / Scrambles
Function / homology
Function and homology information


regulation of axon diameter / sperm mitochondrion organization / brain-derived neurotrophic factor receptor signaling pathway / intracellular magnesium ion homeostasis / neuronal dense core vesicle lumen / lysosomal protein catabolic process / protein retention in Golgi apparatus / response to environmental enrichment / microglia differentiation / neuroinflammatory response ...regulation of axon diameter / sperm mitochondrion organization / brain-derived neurotrophic factor receptor signaling pathway / intracellular magnesium ion homeostasis / 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 / regulation of cell size / lipid transport / flagellated sperm motility / protein secretion / social behavior / amino acid transport / multicellular organism growth / skeletal muscle fiber development / adult locomotory behavior / myelination / lipid droplet / erythrocyte differentiation / Peptide ligand-binding receptors / intracellular calcium ion homeostasis / mitochondrial membrane / gene expression / autophagy / intracellular protein localization / sperm midpiece / mitochondrial outer membrane / protein-macromolecule adaptor activity / endosome membrane / neuron projection / lysosomal membrane / neuronal cell body / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
: / XK-related protein / XK-related protein / 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 ...: / XK-related protein / XK-related protein / 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
Endoplasmic reticulum membrane adapter protein XK / Intermembrane lipid transfer protein VPS13A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsHu, B. / Reinisch, K.M.
Funding support United States, 1items
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, 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
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Endoplasmic reticulum membrane adapter protein XK
B: Intermembrane lipid transfer protein VPS13A


Theoretical massNumber of molelcules
Total (without water)235,0712
Polymers235,0712
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 Endoplasmic reticulum membrane adapter protein XK / Kell complex 37 kDa component / Kx antigen / Membrane transport protein XK / XK-related protein 1


Mass: 50946.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XK, XKR1, XRG1 / Production host: Homo sapiens (human) / References: UniProt: P51811
#2: Protein Intermembrane lipid transfer protein VPS13A / Chorea-acanthocytosis protein / Chorein / Vacuolar protein sorting-associated protein 13A


Mass: 184124.172 Da / Num. of mol.: 1 / Fragment: residues 1550-3174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS13A, CHAC, KIAA0986 / Production host: Homo sapiens (human) / References: UniProt: Q96RL7
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

ComponentName: VPS13A/Calmodulin-XKR1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCv4.6.2particle selectionBlob-based picking and template-based picking
2PHENIX1.21.2_5419:model refinement
5cryoSPARCv4.6.2CTF correctionPatch CTF Estimation
10cryoSPARCv4.6.2initial Euler assignmentAb-initio
11cryoSPARCv4.6.2final Euler assignment
13cryoSPARCv4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 385639 / Symmetry type: POINT

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