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- EMDB-72913: VPS13A/Ct-XKR1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72913
TitleVPS13A/Ct-XKR1
Map data
Sample
  • Complex: VPS13A/Calmodulin-XKR1 complex
    • Protein or peptide: Endoplasmic reticulum membrane adapter protein XK
    • Protein or peptide: Intermembrane lipid transfer protein VPS13A
KeywordsVPS13A / XKR1 / BLTPs / Scrambles / LIPID TRANSPORT
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 / protein retention in Golgi apparatus / mitochondria-associated endoplasmic reticulum membrane contact site / lysosomal protein catabolic process / Golgi to endosome transport / 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 / 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 / regulation of cell size / lipid transport / motor behavior / exploration behavior / amino acid transport / protein secretion / social behavior / skeletal muscle fiber development / myelination / lipid droplet / Peptide ligand-binding receptors / erythrocyte differentiation / adult locomotory behavior / autophagy / multicellular organism growth / mitochondrial membrane / intracellular calcium ion homeostasis / intracellular protein localization / sperm midpiece / gene expression / protein-macromolecule adaptor activity / mitochondrial outer membrane / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsHu B / Reinisch KM
Funding support United States, 1 items
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 KM
History
DepositionSep 27, 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_72913.png

Downloads & links

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Map

FileDownload / File: emd_72913.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 672 pix.
= 559.104 Å		0.83 Å/pix.
x 672 pix.
= 559.104 Å		0.83 Å/pix.
x 672 pix.
= 559.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0
Minimum - Maximum-52.270119999999999 - 89.406930000000003
Average (Standard dev.)0.00000000000076 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 559.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72913_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72913_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VPS13A/Calmodulin-XKR1 complex

EntireName: VPS13A/Calmodulin-XKR1 complex
Components
  • Complex: VPS13A/Calmodulin-XKR1 complex
    • Protein or peptide: Endoplasmic reticulum membrane adapter protein XK
    • Protein or peptide: Intermembrane lipid transfer protein VPS13A

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Supramolecule #1: VPS13A/Calmodulin-XKR1 complex

SupramoleculeName: VPS13A/Calmodulin-XKR1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Endoplasmic reticulum membrane adapter protein XK

MacromoleculeName: Endoplasmic reticulum membrane adapter protein XK / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.946895 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFPASVLAS VFLFVAETTA ALSLSSTYRS GGDRMWQALT LLFSLLPCAL VQLTLLFVHR DLSRDRPLVL LLHLLQLGPL FRCFEVFCI YFQSGNNEEP YVSITKKRQM PKNGLSEEIE KEVGQAEGKL ITHRSAFSRA SVIQAFLGSA PQLTLQLYIS V MQQDVTVG ...String:
MKFPASVLAS VFLFVAETTA ALSLSSTYRS GGDRMWQALT LLFSLLPCAL VQLTLLFVHR DLSRDRPLVL LLHLLQLGPL FRCFEVFCI YFQSGNNEEP YVSITKKRQM PKNGLSEEIE KEVGQAEGKL ITHRSAFSRA SVIQAFLGSA PQLTLQLYIS V MQQDVTVG RSLLMTISLL SIVYGALRCN ILAIKIKYDE YEVKVKPLAY VCIFLWRSFE IATRVVVLVL FTSVLKTWVV VI ILINFFS FFLYPWILFW CSGSPFPENI EKALSRVGTT IVLCFLTLLY TGINMFCWSA VQLKIDSPDL ISKSHNWYQL LVY YMIRFI ENAILLLLWY LFKTDIYMYV CAPLLVLQLL IGYCTAILFM LVFYQFFHPC KKLFSSSVSE GFQRWLRCFC WACR QQKPC EPIGKEDLQS SRDRDETPSS SKTSPEPGQF LNAEDLCSA

UniProtKB: Endoplasmic reticulum membrane adapter protein XK

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Macromolecule #2: Intermembrane lipid transfer protein VPS13A

MacromoleculeName: Intermembrane lipid transfer protein VPS13A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 184.124172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VKWEINVIIK NPEIVFVADM TKNDAPALVI TTQCEICYKG NLENSTMTAA IKDLQVRACP FLPVKRKGKI TTVLQPCDLF YQTTQKGTD PQVIDMSVKS LTLKVSPVII NTMITITSAL YTTKETIPEE TASSTAHLWE KKDTKTLKMW FLEESNETEK I APTTELVP ...String:
VKWEINVIIK NPEIVFVADM TKNDAPALVI TTQCEICYKG NLENSTMTAA IKDLQVRACP FLPVKRKGKI TTVLQPCDLF YQTTQKGTD PQVIDMSVKS LTLKVSPVII NTMITITSAL YTTKETIPEE TASSTAHLWE KKDTKTLKMW FLEESNETEK I APTTELVP KGEMIKMNID SIFIVLEAGI GHRTVPMLLA KSRFSGEGKN WSSLINLHCQ LELEVHYYNE MFGVWEPLLE PL EIDQTED FRPWNLGIKM KKKAKMAIVE SDPEEENYKV PEYKTVISFH SKDQLNITLS KCGLVMLNNL VKAFTEAATG SSA DFVKDL APFMILNSLG LTISVSPSDS FSVLNIPMAK SYVLKNGESL SMDYIRTKDN DHFNAMTSLS SKLFFILLTP VNHS TADKI PLTKVGRRLY TVRHRESGVE RSIVCQIDTV EGSKKVTIRS PVQIRNHFSV PLSVYEGDTL LGTASPENEF NIPLG SYRS FIFLKPEDEN YQMCEGIDFE EIIKNDGALL KKKCRSKNPS KESFLINIVP EKDNLTSLSV YSEDGWDLPY IMHLWP PIL LRNLLPYKIA YYIEGIENSV FTLSEGHSAQ ICTAQLGKAR LHLKLLDYLN HDWKSEYHIK PNQQDISFVS FTCVTEM EK TDLDIAVHMT YNTGQTVVAF HSPYWMVNKT GRMLQYKADG IHRKHPPNYK KPVLFSFQPN HFFNNNKVQL MVTDSELS N QFSIDTVGSH GAVKCKGLKM DYQVGVTIDL SSFNITRIVT FTPFYMIKNK SKYHISVAEE GNDKWLSLDL EQCIPFWPE YASSKLLIQV ERSEDPPKRI YFNKQENCIL LRLDNELGGI IAEVNLAEHS TVITFLDYHD GAATFLLINH TKNELVQYNQ SSLSEIEDS LPPGKAVFYT WADPVGSRRL KWRCRKSHGE VTQKDDMMMP IDLGEKTIYL VSFFEGLQRI ILFTEDPRVF K VTYESEKA ELAEQEIAVA LQDVGISLVN NYTKQEVAYI GITSSDVVWE TKPKKKARWK PMSVKHTEKL EREFKEYTES SP SEDKVIQ LDTNVPVRLT PTGHNMKILQ PHVIALRRNY LPALKVEYNT SAHQSSFRIQ IYRIQIQNQI HGAVFPFVFY PVK PPKSVT MDSAPKPFTD VSIVMRSAGH SQISRIKYFK VLIQEMDLRL DLGFIYALTD LMTEAEVTEN TEVELFHKDI EAFK EEYKT ASLVDQSQVS LYEYFHISPI KLHLSVSLSS GREEAKDSKQ NGGLIPVHSL NLLLKSIGAT LTDVQDVVFK LAFFE LNYQ FHTTSDLQSE VIRHYSKQAI KQMYVLILGL DVLGNPFGLI REFSEGVEAF FYEPYQGAIQ GPEEFVEGMA LGLKAL VGG AVGGLAGAAS KITGAMAKGV AAMTMDEDYQ QKRREAMNKQ PAGFREGITR GGKGLVSGFV SGITGIVTKP IKGAQKG GA AGFFKGVGKG LVGAVARPTG GIIDMASSTF QGIKRATETS EVESLRPPRF FNEDGVIRPY RLRDGTGNQM LQVMENGR F AKYKYFTHVM INKTDMLMIT RRGVLFVTKG TFGQLTCEWQ YSFDEFTKEP FIVHGRRLRI EAKERVKSVF HAREFGKII NFKTPEDARW ILTKLQEARE PSPSL

UniProtKB: Intermembrane lipid transfer protein VPS13A

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.2) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 385639
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
FSC plot (resolution estimation)

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