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- EMDB-21113: Cryo EM Structure of VPS13 protein, 1-1390 from C. thermophilum, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21113
TitleCryo EM Structure of VPS13 protein, 1-1390 from C. thermophilum, in complex with calmodulin
Map dataVPS13 protein
Sample
  • Complex: Chaetomium thermophilum VPS13 1-1390 in complex with calmodulin
    • Complex: VPS13 (1-1390)
      • Protein or peptide: Vacuolar protein sorting-associate protein 13
    • Complex: calmodulin
      • Protein or peptide: Calmodulin-1
KeywordsChorein-N / membrane contact sites / lipid transport / lipid homeostasis
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 / calyx of Held / Ras activation upon Ca2+ influx through NMDA receptor / adenylate cyclase activator activity / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / sarcomere / 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 / long-term synaptic potentiation / Platelet degranulation / 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 speciesChaetomium thermophilum (fungus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsLi P / Lees JA / Reinisch KM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131715 United States
CitationJournal: J Cell Biol / Year: 2020
Title: Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes.
Authors: PeiQi Li / Joshua Aaron Lees / C Patrick Lusk / Karin M Reinisch /
Abstract: A single particle cryo-EM reconstruction of an ∼160-kD N-terminal fragment of the lipid transport protein VPS13 reveals an ∼160-Å long channel lined with hydrophobic residues suitable for ...A single particle cryo-EM reconstruction of an ∼160-kD N-terminal fragment of the lipid transport protein VPS13 reveals an ∼160-Å long channel lined with hydrophobic residues suitable for solubilizing multiple lipid fatty acid moieties. The structure suggests that VPS13 and related proteins, like the autophagy protein ATG2, can act as bridges between organelle membranes to allow bulk lipid flow between organelles.
History
DepositionDec 12, 2019-
Header (metadata) releaseMar 11, 2020-
Map releaseMar 11, 2020-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21113.png

Downloads & links

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Map

FileDownload / File: emd_21113.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVPS13 protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 250 pix.
= 262.5 Å		1.05 Å/pix.
x 250 pix.
= 262.5 Å		1.05 Å/pix.
x 250 pix.
= 262.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.088452674 - 0.14294113
Average (Standard dev.)0.000011978827 (±0.0029231927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 262.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z262.500262.500262.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0880.1430.000

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Supplemental data

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Sample components

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Entire : Chaetomium thermophilum VPS13 1-1390 in complex with calmodulin

EntireName: Chaetomium thermophilum VPS13 1-1390 in complex with calmodulin
Components
  • Complex: Chaetomium thermophilum VPS13 1-1390 in complex with calmodulin
    • Complex: VPS13 (1-1390)
      • Protein or peptide: Vacuolar protein sorting-associate protein 13
    • Complex: calmodulin
      • Protein or peptide: Calmodulin-1

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Supramolecule #1: Chaetomium thermophilum VPS13 1-1390 in complex with calmodulin

SupramoleculeName: Chaetomium thermophilum VPS13 1-1390 in complex with calmodulin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: C. thermophilum VPS13 (1-1390), overexpressed from Expi293F cells copurifies with endogenous calmodulin
Molecular weightTheoretical: 161.84 kDa/nm

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Supramolecule #2: VPS13 (1-1390)

SupramoleculeName: VPS13 (1-1390) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Chaetomium thermophilum (fungus)

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Supramolecule #3: calmodulin

SupramoleculeName: calmodulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Vacuolar protein sorting-associate protein 13

MacromoleculeName: Vacuolar protein sorting-associate protein 13 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKLAAA LE GLVAGLLNRF LGMYVKNFDP KQLKWEVWNG KVRLDNLELQ REALDQLKLP INVIKGHLGH LVLHIPW KT LASEQVKINI EDVFLLASPK EEAEYDEDEE ARRRHRLKME KLDSAELLKE RSQEGLSEEE QKRTQTFA Q ...String:
MDYKDHDGDY KDHDIDYKDD DDKLAAA LE GLVAGLLNRF LGMYVKNFDP KQLKWEVWNG KVRLDNLELQ REALDQLKLP INVIKGHLGH LVLHIPW KT LASEQVKINI EDVFLLASPK EEAEYDEDEE ARRRHRLKME KLDSAELLKE RSQEGLSEEE QKRTQTFA Q ALVTKIVDNL QITIRNIHIR YEDAISAPGH PFALGITLEE FSAVSTDSDW TPAFITSIQS AHKLATLES LAIYWDTDAK LIGPGREPHE HSDQIPHDEM LKFFREMIAK GEADLSSEHQ FILKPVSGQA KIEIDKTGSH TVPRYKANL LFDEIGVVLD DQQYRDALMM VDLFHYFIRH QEYKKFQPKG VTPKEDPRAW FRFAGNAVLS K IHERNRRW SWDYFRERRD DRRRYIELFK KTKQNIQLTP EEREDLDKLE WKLSYEDLRF WRSLARNQLK KE NAEALKN KPPPQPQQQQ GWLSWVWGSK PVQPQQEEQQ GDENTRITEA QRKELYEVIQ WDEKAALAAE IDV PRDSVR LLIETSLSTG SFTLRQNPHG DARDLISLHF DLFRAKGLTR PDSFLIDISL GGFRVNDNTT PDSL YKEIV RVKDAPNTEG QKRYSIADLE LTVDEEAFFE LQVEQHPLDG QGDVAVTMKL KPLEIIWNPN VVVGI ADFF RPPERHMESI NALLETANAT VEGLRAQTRA GLQFALEEHK TVNAKLDLQA PLIILPESIT TPNSTC LIV DAGHISVNSE LVDKETMKQV QSTQDRPCTE EDLRRLEELM YDRFLVKLTS TQVLIGPSVE ITKQQLV QR DEKRQLHIVD QINLDFVVAM SILPKAPNLT KLKISGHLPV LQVNASDSKY KHLMRIIEVA IPKLYDVE P VLAPSGSHPT IRPRLASDAS TRSRRASFRK ASTQFLQFVS QQQEIVLDES DSDDDSEKFE DAKDTSVDE QLRIQQRIFD FKFTVDQLRG SLYRSDPEGK HPDQLLVELV AENFGVEYHL RPYDMSAMVS LGSVTMDDFV ENPPAEFKS IVSSGDIEDR KQARDLVRVK FVRVKKESPE FMSVYDGIET NVDVAISTIN LVVTRKTLLT L LDFILVTF SNPQPAAPVA TRMAVTDQES ETNIIVQPPP IESGPIRVKV DLKSIRMILN NDGIRLATLS FN HADVGVY ILGRYMRVSA KLGDLSLVDD VNLGVSEDSS LRQLVTIQGN ELADFRYEYF DPDKPEKNPG YDS SIYLRA GSVKVNFIEE PFRKIVDFLV KFGKMQAIYN AARMAAANQA QQLQQSQSRI KFDIVVKTPI VVFP RVVMS PKPKRDVITA YLGEIYAQNA FVPLDDSEKA DMAMKLTTGI RNIRLTSHFH YSEGRDEVLE LIDHV DLGF TIIYAEHKEG IKRPDLEIEG SMSDFNLRIT PYQLSALLAI SQSVPTVFAA DVEQHT

UniProtKB: Intermembrane lipid transfer protein VPS13

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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 / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 175364
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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