7TAP: Archazolid A

Cryo-EM structure of archazolid A bound to yeast VO V-ATPase. Determined by electron microscopy at 2.8 Å resolution. Released 23 Feb 2022.

Method
Electron microscopy
Resolution
2.8 Å
Organism
Saccharomyces cerevisiae
Chains
15
Atoms
22,520
Mol. weight
359.33 kDa
Ligands
KJL
Released
23 Feb 2022

Explore 7TAP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TAP contains 128 α-helices and 23 β-strands across 15 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: 41 helices, 20 β-strands

ElementResiduesLengthSheet
α-helix4-63
α-helix11-133
β-strand14-2293
α-helix23-3614
β-strand3914
β-strand40-4123
α-helix50-523
α-helix56-7823
α-helix100-1034
α-helix104-14643
α-helix149-1524
β-strand186-19275
α-helix193-20715
β-strand214-21745
α-helix2211
β-strand222-22436
β-strand229-23136
β-strand233-23975
α-helix243-25513
β-strand258-26145
α-helix267-32458
β-strand327-32933
β-strand334-34293
α-helix343-36018
β-strand369-37133
α-helix3771
β-strand378-37927
α-helix387-39711
α-helix399-4013
α-helix404-4063
α-helix408-42316
α-helix426-44116
α-helix443-4486
α-helix453-4608
α-helix462-47918
β-strand48218
β-strand48518
β-strand494-49529
β-strand506-50721
β-strand509-51029
α-helix520-5223
α-helix528-56134
α-helix565-5673
α-helix568-5725
α-helix573-5797
α-helix580-5845
α-helix585-59511
α-helix598-6014
α-helix608-61710
α-helix630-65829
α-helix707-73226
α-helix735-75016
α-helix751-7555
α-helix757-7604
α-helix763-78220
α-helix783-7886
α-helix789-79911
α-helix800-8056
α-helix806-8094
β-strand815-81627
β-strand82014
Chain B: 21 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-65
α-helix11-2212
α-helix27-348
α-helix39-479
α-helix65-8521
α-helix90-11526
α-helix120-1256
α-helix129-1313
α-helix137-1404
α-helix145-1484
α-helix149-1535
α-helix159-1613
α-helix174-19825
α-helix2011
α-helix204-22926
α-helix235-2395
α-helix251-2577
α-helix262-27110
α-helix273-2753
α-helix284-29916
α-helix307-33125
Chain C: 9 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix17-3822
α-helix42-443
α-helix47-537
α-helix56-9035
α-helix96-994
α-helix101-12222
α-helix127-1293
α-helix136-17641
α-helix178-20528
Chain D: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix15-4935
α-helix53-553
α-helix58-603
α-helix61-8222
α-helix92-12635
α-helix133-16331
Chain E: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-4335
α-helix47-493
α-helix50-534
α-helix55-7521
α-helix84-11936
α-helix125-15127
Chains F, G, J and L: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-4335
α-helix47-493
α-helix55-7521
α-helix84-11936
α-helix125-15430
Chain H: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-4335
α-helix47-493
α-helix55-7622
α-helix84-11936
α-helix123-1253
α-helix126-15429
Chain I: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-4234
α-helix47-493
α-helix52-543
α-helix55-7622
α-helix84-11936
α-helix125-15430

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
V-type proton ATPase subunit c'Dprotein164Saccharomyces cerevisiaeP32842 (AlphaFold model)
V-type proton ATPase subunit c''Cprotein213Saccharomyces cerevisiaeP23968 (AlphaFold model)
V0 assembly protein 1Nprotein265Saccharomyces cerevisiaeP53262 (AlphaFold model)
V-type proton ATPase subunit eMprotein73Saccharomyces cerevisiaeQ3E7B6 (AlphaFold model)
V-type proton ATPase subunit cE, F, G, H, I, J, K, Lprotein160Saccharomyces cerevisiaeP25515
Yeast V-ATPase subunit fOprotein85Saccharomyces cerevisiaeP0C5R9
V-type proton ATPase subunit dBprotein345Saccharomyces cerevisiaeP32366
V-type proton ATPase subunit a, vacuolar isoformAprotein840Saccharomyces cerevisiaeP32563
Sequence of entity 1 (D), FASTA
>7TAP_1 V-type proton ATPase subunit c' (chains D)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE
Sequence of entity 2 (C), FASTA
>7TAP_2 V-type proton ATPase subunit c'' (chains C)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ
Sequence of entity 3 (N), FASTA
>7TAP_3 V0 assembly protein 1 (chains N)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN
Sequence of entity 4 (M), FASTA
>7TAP_4 V-type proton ATPase subunit e (chains M)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE
Sequence of entity 5 (E, F, G, H, I, J, K, L), FASTA
>7TAP_5 V-type proton ATPase subunit c (chains E, F, G, H, I, J, K, L)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC
Sequence of entity 6 (O), FASTA
>7TAP_6 Yeast V-ATPase subunit f (chains O)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR
Sequence of entity 7 (B), FASTA
>7TAP_7 V-type proton ATPase subunit d (chains B)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY
Sequence of entity 8 (A), FASTA
>7TAP_8 V-type proton ATPase subunit a, vacuolar isoform (chains A)
MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEER
LIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAI
GASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFS
HGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELY
AIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARL
GIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFA
IMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYN
DIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLS
ILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVK
DGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTH
KKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTI
EFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFAL
TCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

Ligands and cofactors

IDNameFormulaCopies
KJLArchazolid AC42 H62 N2 O7 S8

Primary citation

Cryo-EM of the Yeast V O Complex Reveals Distinct Binding Sites for Macrolide V-ATPase Inhibitors. Keon, K.A., Benlekbir, S., Kirsch, S.H. et al. ACS Chem Biol (2022) 17:619-628. DOI 10.1021/acschembio.1c00894 · PubMed

Other PDB entries of the same protein (UniProt P32842 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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