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- EMDB-73344: Cryo-EM structure of the VPS13C C-terminal region -

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Basic information

Entry
Database: EMDB / ID: EMD-73344
TitleCryo-EM structure of the VPS13C C-terminal region
Map dataProcessed by Spisonet; sharpened; flipped
Sample
  • Complex: Purified VPS13C bound to endogenous Calmodulin from Expi293F cells.
    • Complex: VPS13C
      • Protein or peptide: Intermembrane lipid transfer protein VPS13C
    • Complex: Calmodulin
KeywordsLipid transport protein / BLTP / membrane repair / membrane homeostasis / VPS13C / 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 / lipid transport / lipid droplet / mitochondrion organization / response to insulin / late endosome ...dense core granule membrane / negative regulation of type 2 mitophagy / protein retention in Golgi apparatus / Golgi to endosome transport / protein targeting to vacuole / lipid transport / lipid droplet / mitochondrion organization / response to insulin / late endosome / late endosome membrane / mitochondrial outer membrane / lysosome / lysosomal membrane / endoplasmic reticulum membrane / extracellular exosome / cytoplasm / 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 VPS13C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 15, 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_73344.png

Downloads & links

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Map

FileDownload / File: emd_73344.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProcessed by Spisonet; sharpened; flipped
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: 0.35
Minimum - Maximum-3.9442775 - 5.7991114
Average (Standard dev.)-0.00023151918 (±0.034846496)
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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Mask #1

Fileemd_73344_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: original, unsharpened map for VPS13C C-terminus, flipped

Fileemd_73344_additional_1.map
Annotationoriginal, unsharpened map for VPS13C C-terminus, flipped
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B for VPS13C C-terminus, flipped.

Fileemd_73344_half_map_1.map
AnnotationHalf map B for VPS13C C-terminus, flipped.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A for VPS13C C-terminus, flipped.

Fileemd_73344_half_map_2.map
AnnotationHalf map A for VPS13C C-terminus, flipped.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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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.
Molecular weightTheoretical: 442 KDa

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Supramolecule #2: VPS13C

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

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Supramolecule #3: Calmodulin

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

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Macromolecule #1: Intermembrane lipid transfer protein VPS13C

MacromoleculeName: Intermembrane lipid transfer protein VPS13C / type: protein_or_peptide / ID: 1 / 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

Concentration0.04 mg/mL
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 correctionDetails: PathCTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 403001
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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