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- EMDB-72912: VPS13A/Nt-CaM -

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Basic information

Entry
Database: EMDB / ID: EMD-72912
TitleVPS13A/Nt-CaM
Map data
Sample
  • Complex: VPS13A/Calmodulin-XKR1 complex
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: Intermembrane lipid transfer protein VPS13A
KeywordsVPS13A / Calmodulin / Complex / ER / LIPID TRANSPORT
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 / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / neuromuscular process controlling balance / 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 / motor behavior / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / exploration behavior / 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 / protein secretion / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / social behavior / 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 / titin binding / Protein methylation / 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 / calyx of Held / Ras activation upon Ca2+ influx through NMDA receptor / adenylate cyclase activator activity / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / regulation of cytokinesis / protein serine/threonine kinase activator activity / spindle microtubule / erythrocyte differentiation / positive regulation of receptor signaling pathway via JAK-STAT / sarcomere / Translocation of SLC2A4 (GLUT4) to the plasma membrane / adult locomotory behavior / calcium channel regulator activity / Transcriptional activation of mitochondrial biogenesis / RAF activation / response to calcium ion
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 VPS13A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 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_72912.png

Downloads & links

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Map

FileDownload / File: emd_72912.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.5
Minimum - Maximum-53.386932000000002 - 132.983139999999992
Average (Standard dev.)0.000000000000944 (±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_72912_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_72912_half_map_2.map
Projections & Slices
AxesZYX

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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: Calmodulin-1
    • 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: 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
Recombinant expressionOrganism: Homo sapiens (human)
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 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: 92.066148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVFESVVVDV LNRFLGDYVV DLDTSQLSLG IWKGAVALKN LQIKENALSQ LDVPFKVKVG HIGNLKLIIP WKNLYTQPVE AVLEEIYLL IVPSSRIKYD PLKEEKQLME AKQQELKRIE EAKQKVVDQE QHLPEKQDTF AEKLVTQIIK NLQVKISSIH I RYEDDITN ...String:
MVFESVVVDV LNRFLGDYVV DLDTSQLSLG IWKGAVALKN LQIKENALSQ LDVPFKVKVG HIGNLKLIIP WKNLYTQPVE AVLEEIYLL IVPSSRIKYD PLKEEKQLME AKQQELKRIE EAKQKVVDQE QHLPEKQDTF AEKLVTQIIK NLQVKISSIH I RYEDDITN RDKPLSFGIS LQNLSMQTTD QYWVPCLHDE TEKLVRKLIR LDNLFAYWNV KSQMFYLSDY DNSLDDLKNG IV NENIVPE GYDFVFRPIS ANAKLVMNRR SDFDFSAPKI NLEIELHNIA IEFNKPQYFS IMELLESVDM MAQNLPYRKF KPD VPLHHH AREWWAYAIH GVLEVNVCPR LWMWSWKHIR KHRQKVKQYK ELYKKKLTSK KPPGELLVSL EELEKTLDVF NITI ARQTA EVEVKKAGYK IYKEGVKDPE DNKGWFSWLW SWSEQNTNEQ QPDVQPETLE EMLTPEEKAL LYEAIGYSET AVDPT LLKT FEALKFFVHL KSMSIVLREN HQKPELVDIV IEEFSTLIVQ RPGAQAIKFE TKIDSFHITG LPDNSEKPRL LSSLDD AMS LFQITFEINP LDETVSQRCI IEAEPLEIIY DARTVNSIVE FFRPPKEVHL AQLTAATLTK LEEFRSKTAT GLLYIIE TQ KVLDLKINLK ASYIIVPQDG IFSPTSNLLL LDLGHLKVTS KSRSELPDVK QGEANLKEIM DRAYDSFDIQ LTSVQLLY S RVGDNWREAR KLSVSTQHIL VPMHFNLELS KAMVFMDVRM PKFKIYGKLP LISLRISDKK LQGIMELIES IP

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: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 464055
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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