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- PDB-9umg: Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1) -

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Basic information

Entry
Database: PDB / ID: 9umg
TitleCryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)
Components
  • (Vacuolar transporter chaperone complex subunit ...) x 3
  • Vacuolar transporter chaperone 3 complex subunit 3
  • Vacuole transporter chaperone complex subunit 5
KeywordsTRANSPORT PROTEIN / Transporter / Complex / polyP synthesis / Vacuolar membrane
Function / homology
Function and homology information


vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / vacuole fusion, non-autophagic / polyphosphate metabolic process / vacuolar transport / intracellular phosphate ion homeostasis ...vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / vacuole fusion, non-autophagic / polyphosphate metabolic process / vacuolar transport / intracellular phosphate ion homeostasis / fungal-type vacuole membrane / inositol hexakisphosphate binding / vacuolar membrane / autophagosome membrane / cell periphery / cytoplasmic vesicle / cell cortex / nuclear membrane / calmodulin binding / mRNA binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Domain of unknown function DUF202 / VTC domain / VTC domain superfamily / : / Domain of unknown function (DUF202) / VTC domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Vacuole transporter chaperone complex subunit 5 / Vacuolar transporter chaperone complex subunit 1 / Vacuolar transporter chaperone complex subunit 4 / Vacuolar transporter chaperone 3 complex subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsZhang, J. / Du, Z. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32422041 China
CitationJournal: Sci China Life Sci / Year: 2026
Title: Mechanistic insights into the regulation of polyphosphate polymerase VTC by the accessory subunit Vtc5
Authors: Zhang, J. / Du, Z. / Cheng, M. / Zheng, Z. / Jiang, L. / Chen, Y. / Yin, P. / Liu, Z.
History
DepositionApr 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar transporter chaperone complex subunit 1
B: Vacuolar transporter chaperone complex subunit 1
C: Vacuolar transporter chaperone complex subunit 1
D: Vacuolar transporter chaperone complex subunit 4
E: Vacuolar transporter chaperone 3 complex subunit 3
F: Vacuole transporter chaperone complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,7519
Polymers178,7706
Non-polymers1,9803
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Vacuolar transporter chaperone complex subunit ... , 3 types, 4 molecules ABCD

#1: Protein Vacuolar transporter chaperone complex subunit 1 / Negative regulator of CDC42 protein 1 / Phosphate metabolism protein 4 / SPX-dependent ...Negative regulator of CDC42 protein 1 / Phosphate metabolism protein 4 / SPX-dependent polyphosphate polymerase VTC subunit 1 / Vacuolar membrane polyphosphate polymerase accessory subunit 1 / PolyP polymerase


Mass: 13253.810 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: VTC1, NRF1, PHM4, YER072W / Production host: Homo sapiens (human) / References: UniProt: P40046
#2: Protein Vacuolar transporter chaperone complex subunit 1 / Negative regulator of CDC42 protein 1 / Phosphate metabolism protein 4 / SPX-dependent ...Negative regulator of CDC42 protein 1 / Phosphate metabolism protein 4 / SPX-dependent polyphosphate polymerase VTC subunit 1 / Vacuolar membrane polyphosphate polymerase accessory subunit 1 / PolyP polymerase


Mass: 11592.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: VTC1, NRF1, PHM4, YER072W / Production host: Homo sapiens (human) / References: UniProt: P40046
#3: Protein Vacuolar transporter chaperone complex subunit 4 / Phosphate metabolism protein 3 / Polyphosphate kinase / SPX-dependent polyphosphate polymerase VTC ...Phosphate metabolism protein 3 / Polyphosphate kinase / SPX-dependent polyphosphate polymerase VTC subunit 4 / Vacuolar membrane polyphosphate polymerase catalytic subunit / PolyP polymerase


Mass: 60283.613 Da / Num. of mol.: 1 / Mutation: R264A,R266A,E426A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: VTC4, PHM3, YJL012C, J1345 / Production host: Homo sapiens (human)
References: UniProt: P47075, ATP-polyphosphate phosphotransferase

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Protein , 2 types, 2 molecules EF

#4: Protein Vacuolar transporter chaperone 3 complex subunit 3 / Phosphate metabolism protein 2 / SPX-dependent polyphosphate polymerase VTC subunit 3 / Vacuolar ...Phosphate metabolism protein 2 / SPX-dependent polyphosphate polymerase VTC subunit 3 / Vacuolar membrane polyphosphate polymerase accessory subunit 3 / PolyP polymerase


Mass: 69612.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: VTC3, PHM2, YPL019C / Production host: Homo sapiens (human) / References: UniProt: Q02725
#5: Protein Vacuole transporter chaperone complex subunit 5 / Vacuolar membrane polyphosphate polymerase regulatory subunit 5 / PolyP polymerase


Mass: 12434.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: VTC5, YDR089W, D4495, YD8554.22 / Production host: Homo sapiens (human) / References: UniProt: P38966

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Non-polymers , 1 types, 3 molecules

#6: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vacuolar transporter chaperone (VTC) complex composed of Vtc1, Vtc3, Vtc4 and Vtc5
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 150mM NaCl, 25mM Tris-HCL, 0.0002m/v GDN, 1mM IP6
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mmol/Lsodium chlorideNaCl1
225 mmol/LTris BaseTris-HCL1
30.0002 m/vGlyco-diosgeninGDN1
41 mmol/LPhytic AcidIP61
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
13Coot0.9.8model refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186553 / Symmetry type: POINT
RefinementHighest resolution: 3.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310119
ELECTRON MICROSCOPYf_angle_d0.69513733
ELECTRON MICROSCOPYf_dihedral_angle_d6.4921331
ELECTRON MICROSCOPYf_chiral_restr0.0431566
ELECTRON MICROSCOPYf_plane_restr0.0061672

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