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- EMDB-64273: Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1) -

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Basic information

Entry
Database: EMDB / ID: EMD-64273
TitleCryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)
Map data
Sample
  • Complex: Vacuolar transporter chaperone (VTC) complex composed of Vtc1, Vtc3, Vtc4 and Vtc5
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 1
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 1
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 4
    • Protein or peptide: Vacuolar transporter chaperone 3 complex subunit 3
    • Protein or peptide: Vacuole transporter chaperone complex subunit 5
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsTransporter / Complex / polyP synthesis / Vacuolar membrane / TRANSPORT PROTEIN
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
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 (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsZhang J / Du Z / Liu Z
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64273.png

Downloads & links

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Map

FileDownload / File: emd_64273.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0915
Minimum - Maximum-0.028052596 - 1.9737426
Average (Standard dev.)0.0008871567 (±0.020235939)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64273_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_64273_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 : Vacuolar transporter chaperone (VTC) complex composed of Vtc1, Vt...

EntireName: Vacuolar transporter chaperone (VTC) complex composed of Vtc1, Vtc3, Vtc4 and Vtc5
Components
  • Complex: Vacuolar transporter chaperone (VTC) complex composed of Vtc1, Vtc3, Vtc4 and Vtc5
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 1
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 1
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 4
    • Protein or peptide: Vacuolar transporter chaperone 3 complex subunit 3
    • Protein or peptide: Vacuole transporter chaperone complex subunit 5
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: Vacuolar transporter chaperone (VTC) complex composed of Vtc1, Vt...

SupramoleculeName: Vacuolar transporter chaperone (VTC) complex composed of Vtc1, Vtc3, Vtc4 and Vtc5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: Vacuolar transporter chaperone complex subunit 1

MacromoleculeName: Vacuolar transporter chaperone complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 13.25381 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PLLQRTPGKK IALPTRVEPK VFFANERTFL SWLNFTVMLG GLGVGLLNFG DKIGRVSAGL FTFVAMGTMI YALVTYHWRA AAIRRRGSG PYDDRLGPTL LCFFLLVAVI INFILRLKY

UniProtKB: Vacuolar transporter chaperone complex subunit 1

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Macromolecule #2: Vacuolar transporter chaperone complex subunit 1

MacromoleculeName: Vacuolar transporter chaperone complex subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 11.592723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VEPKVFFANE RTFLSWLNFT VMLGGLGVGL LNFGDKIGRV SAGLFTFVAM GTMIYALVTY HWRAAAIRRR GSGPYDDRLG PTLLCFFLL VAVIINFILR LKYN

UniProtKB: Vacuolar transporter chaperone complex subunit 1

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Macromolecule #3: Vacuolar transporter chaperone complex subunit 4

MacromoleculeName: Vacuolar transporter chaperone complex subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ATP-polyphosphate phosphotransferase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 60.283613 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RQTTKYWVHP DNITELKLII LKHLPVLVFN TNKEFEREDS AITSIYFDNE NLDLYYGRLR KDEGAEAHAL AWYGGMSTDT IFVERKTHR EDWTGEKSVK ARFALKERHV NDFLKGKYTV DQVFAKMRKE GKKPMNEIEN LEALASEIQY VMLKKKLRPV V RSFYNRTA ...String:
RQTTKYWVHP DNITELKLII LKHLPVLVFN TNKEFEREDS AITSIYFDNE NLDLYYGRLR KDEGAEAHAL AWYGGMSTDT IFVERKTHR EDWTGEKSVK ARFALKERHV NDFLKGKYTV DQVFAKMRKE GKKPMNEIEN LEALASEIQY VMLKKKLRPV V RSFYNRTA FQLPGDARVR ISLDTELTMV REDNFDGVDR THKNWRRTDI GVDWPFKQLD DKDICRFPYA VLNVKLQTQL GQ EPPEWVR ELVGSHLVEP VPKFSKFIHG VATLLNDKVD SIPFWLPQMD VDIRKPPLPT NIEITRPGRS DNEDNDFDED DED DAALVA AMTNAPGNSL DIEESVGYGA TSAPTSNTNH VVESANAAYY QRKIRNAENP ISKKYYEIVA FFDHYFNGDQ ISKI PKGTT FDTQIRAPPG KTICVPVRVE PKVYFATERT YLSWLSISIL LGGVSTTLLT YGSPTAMIGS IGFFITSLAV LIRTV MVYA KRVVNIRLKR AVDYEDKIGP GMVSVFLILS ILFSFFCNLV AKL

UniProtKB: Vacuolar transporter chaperone complex subunit 4

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Macromolecule #4: Vacuolar transporter chaperone 3 complex subunit 3

MacromoleculeName: Vacuolar transporter chaperone 3 complex subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 69.612711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ASFKSYKFWV HDDNIMEVKA RILRHLPALV YASVPNENDD FVDNLESDVR VQPEARLNIG SKSNSLSSDG NSNQDVEIGK SKSVIFPQS YDPTITTLYF DNDFFDLYNN RLLKISGAPT LRLRWIGKLL DKPDIFLEKR TFTENTETGN SSFEEIRLQM K AKFINNFI ...String:
ASFKSYKFWV HDDNIMEVKA RILRHLPALV YASVPNENDD FVDNLESDVR VQPEARLNIG SKSNSLSSDG NSNQDVEIGK SKSVIFPQS YDPTITTLYF DNDFFDLYNN RLLKISGAPT LRLRWIGKLL DKPDIFLEKR TFTENTETGN SSFEEIRLQM K AKFINNFI FKNDPSYKNY LINQLRERGT QKEELEKLSR DFDNIQNFIV EEKLQPVLRA TYNRTAFQIP GDQSIRVTID SN IMYIRED SLDKNRPIRN PENWHRDDID SNIPNPLRFL RAGEYSKFPY SVMEIKVINQ DNSQMPNYEW IKDLTNSHLV NEV PKFSLY LQGVASLFGE DDKYVNILPF WLPDLETDIR KNPQEAYEEE KKTLQKQKSI HDKLDNMRRL SKISVPDGKT TERQ GQKDQ NTRHVIADLE DHESSDEEGT ALPKKSAVKK GKKFKTNAAF LKILAGKNIS ENGNDPYSDD TDSASSFQLP PGVKK PVHL LKNAGPVKVE AKVWLANERT FNRWLSVTTL LSVLTFSIYN SVQKAEFPQL ADLLAYVYFF LTLFCGVWAY RTYLKR LTL IKGRSGKHLD APVGPILVAV VLIVTLVVNF SVAFKEAARR E

UniProtKB: Vacuolar transporter chaperone 3 complex subunit 3

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Macromolecule #5: Vacuole transporter chaperone complex subunit 5

MacromoleculeName: Vacuole transporter chaperone complex subunit 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 12.434865 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SIYEYRHDEV VTFLYLSALL TSCIMASVCL GIVLSLFRGQ SNNEIDLEIQ NILIAIIIIS LLVSLILICA CLLLLFSRFT LAPIWHYVG CFTMFFSVTG TVCYGMIEIF F

UniProtKB: Vacuole transporter chaperone complex subunit 5

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Macromolecule #6: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 6 / Number of copies: 3 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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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: 8
Component:
ConcentrationFormulaName
150.0 mmol/LNaClsodium chloride
25.0 mmol/LTris-HCLTris Base
0.0002 m/vGDNGlyco-diosgenin
1.0 mmol/LIP6Phytic Acid

Details: 150mM NaCl, 25mM Tris-HCL, 0.0002m/v GDN, 1mM IP6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186553
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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