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- PDB-9yrm: CryoEM Structure of VPS13 protein, 1-1390 from C. thermophilum, i... -

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Basic information

Entry
Database: PDB / ID: 9yrm
TitleCryoEM Structure of VPS13 protein, 1-1390 from C. thermophilum, in complex with calmodulin
Components
  • Calmodulin-1
  • Intermembrane lipid transfer protein VPS13
KeywordsLIPID TRANSPORT / lipid transport protein / BLTP
Function / homology
Function and homology information


phospholipid transfer activity / protein retention in Golgi apparatus / intermembrane lipid transfer / late endosome to vacuole transport / protein targeting to vacuole / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels ...phospholipid transfer activity / protein retention in Golgi apparatus / intermembrane lipid transfer / late endosome to vacuole transport / protein targeting to vacuole / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / : / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / regulation of cell communication by electrical coupling involved in cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Protein methylation / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / calcium channel complex / substantia nigra development / FCGR3A-mediated IL10 synthesis / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Ras activation upon Ca2+ influx through NMDA receptor / calyx of Held / adenylate cyclase activator activity / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / regulation of cytokinesis / protein serine/threonine kinase activator activity / spindle microtubule / sarcomere / positive regulation of receptor signaling pathway via JAK-STAT / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / mitochondrion organization / Transcriptional activation of mitochondrial biogenesis / RAF activation / phospholipid binding / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Stimuli-sensing channels / spindle pole / calcium-dependent protein binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / RAS processing / Signaling by BRAF and RAF1 fusions / Platelet degranulation / long-term synaptic potentiation / myelin sheath / synaptic vesicle membrane / Inactivation, recovery and regulation of the phototransduction cascade / RAF/MAP kinase cascade
Similarity search - Function
Vacuolar protein sorting-associated protein 13, fungi / 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 ...Vacuolar protein sorting-associated protein 13, fungi / 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 / Cytosolic fatty-acid binding proteins signature. / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Intermembrane lipid transfer protein VPS13 / Calmodulin-1
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsLi, D. / Reinisch, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Aligning Science Across Parkinsons (ASAP)ASAP-000580 United States
CitationJournal: bioRxiv / Year: 2025
Title: Insights into the regulation of VPS13 family bridge-like lipid transfer proteins from the structure of VPS13C.
Authors: Dazhi Li / Xinbo Wang / Bodan Hu / Hongyan Hao / Stephanie Hamill / Yuting Li / Guochao Chen / Pietro De Camilli / Karin M Reinisch /
Abstract: Bridge-like lipid transfer proteins (BLTPs) play central roles in redistributing lipids from their primary site of synthesis in the endoplasmic reticulum to other organelles. They comprise bridge- ...Bridge-like lipid transfer proteins (BLTPs) play central roles in redistributing lipids from their primary site of synthesis in the endoplasmic reticulum to other organelles. They comprise bridge-domains spanning between organelles at contact sites that allow lipids to transit the cytosol between adjacent membranes. The assembly of BLTPs into complexes with adaptor proteins enables their lipid transfer ability. To address the mechanisms underlying assembly and regulation of BLTP complexes, we used cryo-EM to resolve the structure of one such BLTP, the Parkinson's protein VPS13C, at near-atomic resolution. The structure identifies a lipid-transfer-nonpermissive conformation, where the built-in C-terminal VAB adaptor module blocks the end of the lipid transfer bridge, interfering with lipid delivery. We also identify calmodulin, central to calcium signaling, as a VPS13 partner, suggesting calcium regulation of VPS13 function. Altogether, this structure of intact VPS13C serves as starting point to understand its regulation and, more broadly, that of other BLTPs.
History
DepositionOct 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-1
B: Intermembrane lipid transfer protein VPS13


Theoretical massNumber of molelcules
Total (without water)179,0362
Polymers179,0362
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 Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0DP23
#2: Protein Intermembrane lipid transfer protein VPS13 / Vacuolar protein sorting-associated protein 13


Mass: 162183.281 Da / Num. of mol.: 1 / Fragment: residues 1-1390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: VPS13, CTHT_0020450 / Production host: Homo sapiens (human) / References: UniProt: G0S3B8
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

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Cryo-EM Structure of C. thermophilum VPS13 (1-1390) in complex with calmodulinCOMPLEXC. thermophilum VPS13 (1-1390), overexpressed from Expi293F cells copurifies with endogenous calmodulinall0MULTIPLE SOURCES
2VPS13 (1-1390)COMPLEX#21RECOMBINANT
3calmodulinCOMPLEX#11NATURAL
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Thermochaetoides thermophila (fungus)209285
33Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.8
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: 2800 nm / Nominal defocus min: 1900 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2PHENIX1.21.2_5419model refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175364 / Symmetry type: POINT

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