9UMG: VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)

Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1). Determined by electron microscopy at 3.04 Å resolution. Released 21 Jan 2026.

Method
Electron microscopy
Resolution
3.04 Å
Organism
Saccharomyces cerevisiae S288C
Chains
6
Atoms
9,877
Mol. weight
180.75 kDa
Ligands
IHP
Released
21 Jan 2026

Explore 9UMG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9UMG contains 44 α-helices and 30 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 2 β-strands

ElementResiduesLengthSheet
β-strand7-821
β-strand17-1821
α-helix24-5330
α-helix56-8833
α-helix100-11617
α-helix117-1215
Chain B: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix25-5228
α-helix56-8934
α-helix100-12021
Chain C: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix24-5330
α-helix56-8934
α-helix100-12122
Chain D: 16 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand197-20372
α-helix208-2169
β-strand221-22332
β-strand236-24382
α-helix248-2547
β-strand260-26122
β-strand264-26852
β-strand275-285112
β-strand290-300112
α-helix301-3033
α-helix304-3096
α-helix314-3174
α-helix319-3246
α-helix329-34921
β-strand352-364132
β-strand37212
β-strand374-384112
β-strand417-41932
β-strand423-42972
α-helix437-4382
α-helix439-4468
β-strand451-45222
α-helix458-4669
β-strand473-47423
α-helix478-4803
α-helix606-6083
β-strand612-61323
α-helix621-65030
α-helix654-6585
α-helix661-68626
α-helix697-71822
Chain E: 14 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand206-21164
α-helix214-2163
α-helix217-2259
β-strand231-23332
α-helix235-2373
β-strand296-30274
α-helix307-3137
β-strand320-32784
α-helix330-3323
β-strand336-34384
β-strand354-36184
α-helix366-3705
α-helix376-38510
α-helix392-41221
β-strand415-428144
β-strand435-447134
β-strand48115
β-strand48415
β-strand486-48724
β-strand491-49664
α-helix509-5157
β-strand52014
α-helix529-5357
α-helix550-5523
α-helix697-72529
α-helix734-76835
α-helix778-80528
Chain F: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix761-79535
α-helix806-83429
α-helix840-8423
α-helix843-86826

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Vacuolar transporter chaperone complex subunit 1Aprotein118Saccharomyces cerevisiae S288CP40046 (AlphaFold model)
Vacuolar transporter chaperone complex subunit 1B, Cprotein103Saccharomyces cerevisiae S288CP40046 (AlphaFold model)
Vacuolar transporter chaperone complex subunit 4Dprotein527Saccharomyces cerevisiae S288CP47075 (AlphaFold model)
Vacuolar transporter chaperone 3 complex subunit 3Eprotein604Saccharomyces cerevisiae S288CQ02725 (AlphaFold model)
Vacuole transporter chaperone complex subunit 5Fprotein110Saccharomyces cerevisiae S288CP38966 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9UMG_1 Vacuolar transporter chaperone complex subunit 1 (chains A)
PLLQRTPGKKIALPTRVEPKVFFANERTFLSWLNFTVMLGGLGVGLLNFGDKIGRVSAGL
FTFVAMGTMIYALVTYHWRAAAIRRRGSGPYDDRLGPTLLCFFLLVAVIINFILRLKY
Sequence of entity 2 (B, C), FASTA
>9UMG_2 Vacuolar transporter chaperone complex subunit 1 (chains B, C)
VEPKVFFANERTFLSWLNFTVMLGGLGVGLLNFGDKIGRVSAGLFTFVAMGTMIYALVTY
HWRAAAIRRRGSGPYDDRLGPTLLCFFLLVAVIINFILRLKYN
Sequence of entity 3 (D), FASTA
>9UMG_3 Vacuolar transporter chaperone complex subunit 4 (chains D)
RQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLR
KDEGAEAHALAWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVD
QVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRIS
LDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLNVKLQTQLGQ
EPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQMDVDIRKPPLPTNIE
ITRPGRSDNEDNDFDEDDEDDAALVAAMTNAPGNSLDIEESVGYGATSAPTSNTNHVVES
ANAAYYQRKIRNAENPISKKYYEIVAFFDHYFNGDQISKIPKGTTFDTQIRAPPGKTICV
PVRVEPKVYFATERTYLSWLSISILLGGVSTTLLTYGSPTAMIGSIGFFITSLAVLIRTV
MVYAKRVVNIRLKRAVDYEDKIGPGMVSVFLILSILFSFFCNLVAKL
Sequence of entity 4 (E), FASTA
>9UMG_4 Vacuolar transporter chaperone 3 complex subunit 3 (chains E)
ASFKSYKFWVHDDNIMEVKARILRHLPALVYASVPNENDDFVDNLESDVRVQPEARLNIG
SKSNSLSSDGNSNQDVEIGKSKSVIFPQSYDPTITTLYFDNDFFDLYNNRLLKISGAPTL
RLRWIGKLLDKPDIFLEKRTFTENTETGNSSFEEIRLQMKAKFINNFIFKNDPSYKNYLI
NQLRERGTQKEELEKLSRDFDNIQNFIVEEKLQPVLRATYNRTAFQIPGDQSIRVTIDSN
IMYIREDSLDKNRPIRNPENWHRDDIDSNIPNPLRFLRAGEYSKFPYSVMEIKVINQDNS
QMPNYEWIKDLTNSHLVNEVPKFSLYLQGVASLFGEDDKYVNILPFWLPDLETDIRKNPQ
EAYEEEKKTLQKQKSIHDKLDNMRRLSKISVPDGKTTERQGQKDQNTRHVIADLEDHESS
DEEGTALPKKSAVKKGKKFKTNAAFLKILAGKNISENGNDPYSDDTDSASSFQLPPGVKK
PVHLLKNAGPVKVEAKVWLANERTFNRWLSVTTLLSVLTFSIYNSVQKAEFPQLADLLAY
VYFFLTLFCGVWAYRTYLKRLTLIKGRSGKHLDAPVGPILVAVVLIVTLVVNFSVAFKEA
ARRE
Sequence of entity 5 (F), FASTA
>9UMG_5 Vacuole transporter chaperone complex subunit 5 (chains F)
SIYEYRHDEVVTFLYLSALLTSCIMASVCLGIVLSLFRGQSNNEIDLEIQNILIAIIIIS
LLVSLILICACLLLLFSRFTLAPIWHYVGCFTMFFSVTGTVCYGMIEIFF

Ligands and cofactors

IDNameFormulaCopies
IHPInositol hexakisphosphateC6 H18 O24 P63

Primary citation

Mechanistic insights into the regulation of polyphosphate polymerase VTC by the accessory subunit Vtc5. Zhang, J., Du, Z., Cheng, M. et al. Sci China Life Sci (2026) 69:1800-1803. DOI 10.1007/s11427-025-3127-8 · PubMed

Other PDB entries of the same protein (UniProt P40046 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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