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- EMDB-73373: Full-length human VPS13C in complex with calmodulin from the Cryo... -

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Basic information

Entry
Database: EMDB / ID: EMD-73373
TitleFull-length human VPS13C in complex with calmodulin from the CryoEM composite map
Map dataComposite map of full-length VPS13C
Sample
  • Complex: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
    • Complex: VPS13C
      • Protein or peptide: Intermembrane lipid transfer protein VPS13C
    • Complex: Calmodulin
      • Protein or peptide: Calmodulin-1
KeywordsLipid Transport protein / BLTP / lysosomal membrane repair / membrane homeostasis / LIPID TRANSPORT
Function / homology
Function and homology information


dense core granule membrane / negative regulation of type 2 mitophagy / protein retention in Golgi apparatus / Golgi to endosome transport / protein targeting to vacuole / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels ...dense core granule membrane / negative regulation of type 2 mitophagy / protein retention in Golgi apparatus / Golgi to endosome 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 / lipid transport / 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 / lipid droplet / 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 / response to insulin / 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 / late endosome / Platelet degranulation / long-term synaptic potentiation / late endosome membrane
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 / : ...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 / : / 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
Calmodulin-1 / Intermembrane lipid transfer protein VPS13C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.13 Å
AuthorsLi D / Reinisch KM
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73373.png

Downloads & links

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Map

FileDownload / File: emd_73373.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of full-length VPS13C
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 384 pix.
= 546.816 Å		1.42 Å/pix.
x 384 pix.
= 546.816 Å		1.42 Å/pix.
x 384 pix.
= 546.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.424 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.44665444 - 4.407606
Average (Standard dev.)0.0047364114 (±0.034179002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 546.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.

EntireName: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
Components
  • Complex: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
    • Complex: VPS13C
      • Protein or peptide: Intermembrane lipid transfer protein VPS13C
    • Complex: Calmodulin
      • Protein or peptide: Calmodulin-1

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Supramolecule #1: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.

SupramoleculeName: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The plasmid encoding full-length VPS13C with a C-terminal 3xFLAG tag was transfected into Expi293F cells. The VPS13C was transiently expressed. Endogenous calmodulin was co-purified with VPS13C.

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Supramolecule #2: VPS13C

SupramoleculeName: VPS13C / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Calmodulin

SupramoleculeName: Calmodulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #2: Intermembrane lipid transfer protein VPS13C

MacromoleculeName: Intermembrane lipid transfer protein VPS13C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 425.875438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLESVVADL LNRFLGDYVE NLNKSQLKLG IWGGNVALDN LQIKENALSE LDVPFKVKAG QIDKLTLKIP WKNLYGEAVV ATLEGLYLL VVPGASIKYD AVKEEKSLQD VKQKELSRIE EALQKAAEKG THSGEFIYGL ENFVYKDIKP GRKRKKHKKH F KKPFKGLD ...String:
MVLESVVADL LNRFLGDYVE NLNKSQLKLG IWGGNVALDN LQIKENALSE LDVPFKVKAG QIDKLTLKIP WKNLYGEAVV ATLEGLYLL VVPGASIKYD AVKEEKSLQD VKQKELSRIE EALQKAAEKG THSGEFIYGL ENFVYKDIKP GRKRKKHKKH F KKPFKGLD RSKDKPKEAK KDTFVEKLAT QVIKNVQVKI TDIHIKYEDD VTDPKRPLSF GVTLGELSLL TANEHWTPCI LN EADKIIY KLIRLDSLSA YWNVNCSMSY QRSREQILDQ LKNEILTSGN IPPNYQYIFQ PISASAKLYM NPYAESELKT PKL DCNIEI QNIAIELTKP QYLSMIDLLE SVDYMVRNAP YRKYKPYLPL HTNGRRWWKY AIDSVLEVHI RRYTQMWSWS NIKK HRQLL KSYKIAYKNK LTQSKVSEEI QKEIQDLEKT LDVFNIILAR QQAQVEVIRS GQKLRKKSAD TGEKRGGWFS GLWGK KESK KKDEESLIPE TIDDLMTPEE KDKLFTAIGY SESTHNLTLP KQYVAHIMTL KLVSTSVTIR ENKNIPEILK IQIIGL GTQ VSQRPGAQAL KVEAKLEHWY ITGLRQQDIV PSLVASIGDT TSSLLKIKFE TNPEDSPADQ TLIVQSQPVE VIYDAKT VN AVVEFFQSNK GLDLEQITSA TLMKLEEIKE RTATGLTHII ETRKVLDLRI NLKPSYLVVP QTGFHHEKSD LLILDFGT F QLNSKDQGLQ KTTNSSLEEI MDKAYDKFDV EIKNVQLLFA RAEETWKKCR FQHPSTMHIL QPMDIHVELA KAMVEKDIR MARFKVSGGL PLMHVRISDQ KMKDVLYLMN SIPLPQKSSA QSPERQVSSI PIISGGTKGL LGTSLLLDTV ESESDDEYFD AEDGEPQTC KSMKGSELKK AAEVPNEELI NLLLKFEIKE VILEFTKQQK EEDTILVFNV TQLGTEATMR TFDLTVVSYL K KISLDYHE IEGSKRKPLH LISSSDKPGL DLLKVEYIKA DKNGPSFQTA FGKTEQTVKV AFSSLNLLLQ TQALVASINY LT TIIPSDD QSISVAKEVQ ISTEKQQKNS TLPKAIVSSR DSDIIDFRLF AKLNAFCVIV CNEKNNIAEI KIQGLDSSLS LQS RKQSLF ARLENIIVTD VDPKTVHKKA VSIMGNEVFR FNLDLYPDAT EGDLYTDMSK VDGVLSLNVG CIQIVYLHKF LMSL LNFLN NFQTAKESLS AATAQAAERA ATSVKDLAQR SFRVSINIDL KAPVIVIPQS SISTNAVVVD LGLIRVHNQF SLVSD EDYL NPPVIDRMDV QLTKLTLYRT VIQPGIYHPD IQLLHPINLE FLVNRNLAAS WYHKVPVVEI KGHLDSMNVS LNQEDL NLL FRILTENLCE GTEDLDKVKP RVQETGEIKE PLEISISQDV HDSKNTLTTG VEEIRSVDII NMLLNFEIKE VVVTLMK KS EKKGRPLHEL NVLQLGMEAK VKTYDMTAKA YLKKISMQCF DFTDSKGEPL HIINSSNVTD EPLLKMLLTK ADSDGPEF K TIHDSTKQRL KVSFASLDLV LHLEALLSFM DFLSSAAPFS EPSSSEKESE LKPLVGESRS IAVKAVSSNI SQKDVFDLK ITAELNAFNV FVCDQKCNIA DIKIHGMDAS ISVKPKQTDV FARLKDIIVM NVDLQSIHKK AVSILGDEVF RFQLTLYPDA TEGEAYADM SKVDGKLSFK VGCIQIVYVH KFFMSLLNFL NNFQTAKEAL STATVQAAER AASSMKDLAQ KSFRLLMDIN L KAPVIIIP QSSVSPNAVI ADLGLIRVEN KFSLVPMEHY SLPPVIDKMN IELTQLKLSR TILQASLPQN DIEILKPVNM LL SIQRNLA AAWYVQIPGM EIKGKLKPMQ VALSEDDLTV LMKILLENLG EASSQPSPTQ SVQETVRVRK VDVSSVPDHL KEQ EDWTDS KLSMNQIVSL QFDFHFESLS IILYNNDINQ ESGVAFHNDS FQLGELRLHL MASSGKMFKD GSMNVSVKLK TCTL DDLRE GIERATSRMI DRKNDQDNNS SMIDISYKQD KNGSQIDAVL DKLYVCASVE FLMTVADFFI KAVPQSPENV AKETQ ILPR QTATGKVKIE KDDSVRPNMT LKAMITDPEV VFVASLTKAD APALTASFQC NLSLSTSKLE QMMEASVRDL KVLACP FLR EKRGKNITTV LQPCSLFMEK CTWASGKQNI NIMVKEFIIK ISPIILNTVL TIMAALSPKT KEDGSKDTSK EMENLWG IK SINDYNTWFL GVDTATEITE SFKGIEHSLI EENCGVVVES IQVTLECGLG HRTVPLLLAE SKFSGNIKNW TSLMAAVA D VTLQVHYYNE IHAVWEPLIE RVEGKRQWNL RLDVKKNPVQ DKSLLPGDDF IPEPQMAIHI SSGNTMNITI SKSCLNVFN NLAKGFSEGT ASTFDYSLKD RAPFTVKNAV GVPIKVKPNC NLRVMGFPEK SDIFDVDAGQ NLELEYASMV PSSQGNLSIL SRQESSFFT LTIVPHGYTE VANIPVARPG RRLYNVRNPN ASHSDSVLVQ IDATEGNKVI TLRSPLQIKN HFSIAFIIYK F VKNVKLLE RIGIARPEEE FHVPLDSYRC QLFIQPAGIL EHQYKESTTY ISWKEELHRS REVRCMLQCP SVEVSFLPLI VN TVALPDE LSYICTHGED WDVAYIIHLY PSLTLRNLLP YSLRYLLEGT AETHELAEGS TADVLHSRIS GEIMELVLVK YQG KNWNGH FRIRDTLPEF FPVCFSSDST EVTTVDLSVH VRRIGSRMVL SVFSPYWLIN KTTRVLQYRS EDIHVKHPAD FRDI ILFSF KKKNIFTKNK VQLKISTSAW SSSFSLDTVG SYGCVKCPAN NMEYLVGVSI KMSSFNLSRI VTLTPFCTIA NKSSL ELEV GEIASDGSMP TNKWNYIASS ECLPFWPESL SGKLCVRVVG CEGSSKPFFY NRQDNGTLLS LEDLNGGILV DVNTAE HST VITFSDYHEG SAPALIMNHT PWDILTYKQS GSPEEMVLLP RQARLFAWAD PTGTRKLTWT YAANVGEHDL LKDGCGQ FP YDANIQIHWV SFLDGRQRVL LFTDDVALVS KALQAEEMEQ ADYEITLSLH SLGLSLVNNE SKQEVSYIGI TSSGVVWE V KPKQKWKPFS QKQIILLEQS YQKHQISRDH GWIKLDNNFE VNFDKDPMEM RLPIRSPIKR DFLSGIQIEF KQSSHQRSL RARLYWLQVD NQLPGAMFPV VFHPVAPPKS IALDSEPKPF IDVSVITRFN EYSKVLQFKY FMVLIQEMAL KIDQGFLGAI IALFTPTTD PEAERRRTKL IQQDIDALNA ELMETSMTDM SILSFFEHFH ISPVKLHLSL SLGSGGEESD KEKQEMFAVH S VNLLLKSI GATLTDVDDL IFKLAYYEIR YQFYKRDQLI WSVVRHYSEQ FLKQMYVLVL GLDVLGNPFG LIRGLSEGVE AL FYEPFQG AVQGPEEFAE GLVIGVRSLF GHTVGGAAGV VSRITGSVGK GLAAITMDKE YQQKRREELS RQPRDFGDSL ARG GKGFLR GVVGGVTGII TKPVEGAKKE GAAGFFKGIG KGLVGAVARP TGGIVDMASS TFQGIQRAAE STEEVSSLRP PRLI HEDGI IRPYDRQESE GSDLLENHIK KLEGETYRYH CAIPGSKKTI LMVTNRRVLC IKEVEILGLM CVDWQCPFED FVFPP SVSE NVLKISVKEQ GLFHKKDSAN QGCVRKVYLK DTATAERACN AIEDAQSTRQ QQKLMKQSSV RLLRPQLPSL EDYKDH DGD YKDHDIDYKD DDDK

UniProtKB: Intermembrane lipid transfer protein VPS13C

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX / Number images used: 392473
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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