8I6V: Vacuolar transporter chaperone complex subunit 1

Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1). Determined by electron microscopy at 3.06 Å resolution. Released 1 Mar 2023.

Method
Electron microscopy
Resolution
3.06 Å
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains
5
Atoms
13,172
Mol. weight
224.48 kDa
Ligands
MN, 3PO, PO4, POV
Released
1 Mar 2023

Explore 8I6V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I6V contains 67 α-helices and 25 β-strands across 5 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: 3 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix23-5230
α-helix56-8328
α-helix100-12122
Chain B: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix23-5129
α-helix56-8631
α-helix100-12122
Chain C: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix23-5230
α-helix56-8833
α-helix99-12022
Chain D: 32 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix3-97
α-helix13-153
α-helix22-287
α-helix31-355
α-helix46-8641
α-helix96-13338
α-helix139-1402
α-helix142-1509
α-helix160-1612
α-helix162-17312
α-helix174-1785
α-helix188-1947
β-strand205-21281
α-helix217-2259
β-strand231-23332
α-helix235-2373
β-strand246-24722
α-helix294-2952
β-strand296-30271
α-helix307-3137
β-strand320-32781
α-helix330-3323
β-strand336-34491
β-strand353-36191
α-helix366-3705
α-helix376-38813
α-helix392-41221
β-strand415-427131
β-strand435-447131
α-helix475-4784
α-helix479-4802
β-strand484-48631
β-strand490-49781
α-helix508-5147
β-strand519-52131
α-helix527-53610
α-helix551-5533
α-helix561-58323
α-helix584-5885
α-helix697-72529
α-helix728-7303
α-helix734-76633
α-helix778-80427
α-helix823-83311
Chain E: 26 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix3-86
α-helix13-153
α-helix22-3615
α-helix42-8645
α-helix98-13740
α-helix143-15210
α-helix161-17717
β-strand194-203102
α-helix205-2073
α-helix208-2169
β-strand221-22332
β-strand236-24382
α-helix248-2547
β-strand260-26892
β-strand275-28392
β-strand293-30082
α-helix301-3033
α-helix304-3096
α-helix314-3174
α-helix319-3246
α-helix329-34921
β-strand352-366152
β-strand369-384162
α-helix414-4163
β-strand417-41932
β-strand423-432102
α-helix436-4383
α-helix439-4457
β-strand450-45232
α-helix458-4669
β-strand473-47423
α-helix479-4824
α-helix511-52313
α-helix607-6082
β-strand612-61323
α-helix624-64724
α-helix654-6563
α-helix657-68630
α-helix698-71720

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Vacuolar transporter chaperone complex subunit 1A, B, Cprotein129Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P40046 (AlphaFold model)
Vacuolar transporter chaperone 3 complex subunit 3Dprotein835Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Q02725 (AlphaFold model)
Vacuolar transporter chaperone complex subunit 4Eprotein721Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P47075 (AlphaFold model)
Sequence of entity 1 (A, B, C), FASTA
>8I6V_1 Vacuolar transporter chaperone complex subunit 1 (chains A, B, C)
MSSAPLLQRTPGKKIALPTRVEPKVFFANERTFLSWLNFTVMLGGLGVGLLNFGDKIGRV
SAGLFTFVAMGTMIYALVTYHWRAAAIRRRGSGPYDDRLGPTLLCFFLLVAVIINFILRL
KYNDANTKL
Sequence of entity 2 (D), FASTA
>8I6V_2 Vacuolar transporter chaperone 3 complex subunit 3 (chains D)
MLFGIKLANDVYPPWKDSYIDYERLKKLLKESVIHDGRSSVDSWSERNESDFVEALDKEL
EKVYTFQISKYNAVLRKLDDLEENTKSAEKIQKINSEQFKNTLEECLDEAQRLDNFDRLN
FTGFIKIVKKHDKLHPNYPSVKSLLQVRLKELPFNNSEEYSPLLYRISYLYEFLRSNYDH
PNTVSKSLASTSKLSHFSNLEDASFKSYKFWVHDDNIMEVKARILRHLPALVYASVPNEN
DDFVDNLESDVRVQPEARLNIGSKSNSLSSDGNSNQDVEIGKSKSVIFPQSYDPTITTLY
FDNDFFDLYNNRLLKISGAPTLRLRWIGKLLDKPDIFLEKRTFTENTETGNSSFEEIRLQ
MKAKFINNFIFKNDPSYKNYLINQLRERGTQKEELEKLSRDFDNIQNFIVEEKLQPVLRA
TYNRTAFQIPGDQSIRVTIDSNIMYIREDSLDKNRPIRNPENWHRDDIDSNIPNPLRFLR
AGEYSKFPYSVMEIKVINQDNSQMPNYEWIKDLTNSHLVNEVPKFSLYLQGVASLFGEDD
KYVNILPFWLPDLETDIRKNPQEAYEEEKKTLQKQKSIHDKLDNMRRLSKISVPDGKTTE
RQGQKDQNTRHVIADLEDHESSDEEGTALPKKSAVKKGKKFKTNAAFLKILAGKNISENG
NDPYSDDTDSASSFQLPPGVKKPVHLLKNAGPVKVEAKVWLANERTFNRWLSVTTLLSVL
TFSIYNSVQKAEFPQLADLLAYVYFFLTLFCGVWAYRTYLKRLTLIKGRSGKHLDAPVGP
ILVAVVLIVTLVVNFSVAFKEAARRERGLVNVSSQPSLPRTLKPIQDFIFNLVGE
Sequence of entity 3 (E), FASTA
>8I6V_3 Vacuolar transporter chaperone complex subunit 4 (chains E)
MKFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFLESLEIELDKVY
TFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLAKFS
RLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGRP
IKGDSSAGGKQQNFVRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSI
YFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALK
ERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYN
RTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRF
PYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQ
MDVDIRKPPLPTNIEITRPGRSDNEDNDFDEDDEDDAALVAAMTNAPGNSLDIEESVGYG
ATSAPTSNTNHVVESANAAYYQRKIRNAENPISKKYYEIVAFFDHYFNGDQISKIPKGTT
FDTQIRAPPGKTICVPVRVEPKVYFATERTYLSWLSISILLGGVSTTLLTYGSPTAMIGS
IGFFITSLAVLIRTVMVYAKRVVNIRLKRAVDYEDKIGPGMVSVFLILSILFSFFCNLVA
K

Ligands and cofactors

IDNameFormulaCopies
MNManganese (II) ionMn1
3POTriphosphateH5 O10 P31
PO4Phosphate ionO4 P3
POV(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…C42 H82 N O8 P1

Primary citation

Cryo-EM structure of the polyphosphate polymerase VTC reveals coupling of polymer synthesis to membrane transit. Liu, W., Wang, J., Comte-Miserez, V. et al. EMBO J (2023) 42:e113320-e113320. DOI 10.15252/embj.2022113320 · 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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