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- PDB-9yfw: VPS13A central bridge domain -

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Basic information

Entry
Database: PDB / ID: 9yfw
TitleVPS13A central bridge domain
ComponentsIntermembrane lipid transfer protein VPS13A
KeywordsLIPID TRANSPORT / VPS13A / BLTP / RBG motif
Function / homology
Function and homology information


sperm mitochondrion organization / brain-derived neurotrophic factor receptor signaling pathway / neuronal dense core vesicle lumen / protein retention in Golgi apparatus / mitochondria-associated endoplasmic reticulum membrane contact site / lysosomal protein catabolic process / Golgi to endosome transport / neuroinflammatory response / response to environmental enrichment / microglia differentiation ...sperm mitochondrion organization / brain-derived neurotrophic factor receptor signaling pathway / neuronal dense core vesicle lumen / protein retention in Golgi apparatus / mitochondria-associated endoplasmic reticulum membrane contact site / lysosomal protein catabolic process / Golgi to endosome transport / neuroinflammatory response / response to environmental enrichment / microglia differentiation / protein targeting to vacuole / neuron projection arborization / flagellated sperm motility / cellular response to osmotic stress / long-term synaptic depression / neuromuscular process controlling balance / lipid transport / motor behavior / exploration behavior / protein secretion / social behavior / lipid droplet / erythrocyte differentiation / adult locomotory behavior / autophagy / multicellular organism growth / mitochondrial membrane / intracellular protein localization / sperm midpiece / gene expression / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 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: To Be Published
Title: Molecular insights into bulk lipid transport from structural studies of the bridge-like protein VPS13A complexed with the scramblase XKR1
Authors: Hu, B. / Reinisch, K.M.
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
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Intermembrane lipid transfer protein VPS13A


Theoretical massNumber of molelcules
Total (without water)73,4771
Polymers73,4771
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 Intermembrane lipid transfer protein VPS13A / Chorea-acanthocytosis protein / Chorein / Vacuolar protein sorting-associated protein 13A


Mass: 73476.547 Da / Num. of mol.: 1 / Fragment: residues 876-1531
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: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 464055 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047254
ELECTRON MICROSCOPYf_angle_d0.6069832
ELECTRON MICROSCOPYf_dihedral_angle_d4.513949
ELECTRON MICROSCOPYf_chiral_restr0.0471196
ELECTRON MICROSCOPYf_plane_restr0.0051221

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