9MJ4: Yeast V-ATPase Vo proton channel

Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149. Determined by electron microscopy at 3.7 Å resolution. Released 5 Feb 2025.

Method
Electron microscopy
Resolution
3.7 Å
Organisms
Saccharomyces cerevisiae, Lama glama
Chains
16
Atoms
23,018
Mol. weight
368.9 kDa
Released
5 Feb 2025

Explore 9MJ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MJ4 contains 148 α-helices and 37 β-strands across 16 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: 47 helices, 18 β-strands

ElementResiduesLengthSheet
β-strand1015
α-helix11-133
β-strand14-2296
α-helix23-253
α-helix26-3611
β-strand40-4126
α-helix50-523
α-helix56-7823
α-helix81-844
α-helix100-1034
α-helix104-14542
α-helix149-1524
β-strand186-19277
α-helix193-20614
β-strand214-224117
β-strand229-239117
α-helix243-25513
β-strand258-26037
α-helix267-30236
α-helix306-32318
β-strand327-32826
β-strand334-34296
α-helix343-3453
α-helix346-35813
β-strand368-37146
α-helix376-3783
β-strand37918
α-helix385-39511
α-helix399-4013
α-helix4041
β-strand40515
α-helix4061
α-helix408-42316
α-helix426-44116
α-helix443-4464
α-helix453-4608
α-helix462-47817
β-strand48219
β-strand48519
β-strand494-495210
β-strand506-50721
β-strand509-510210
α-helix520-5223
α-helix528-55225
α-helix554-5618
α-helix565-5673
α-helix568-5725
α-helix573-5797
α-helix580-5845
α-helix585-59511
α-helix598-6014
α-helix603-6075
α-helix608-61710
α-helix630-65829
α-helix707-73226
α-helix735-75218
α-helix755-7584
α-helix763-78018
α-helix781-7899
α-helix790-79910
α-helix800-8056
α-helix806-8083
α-helix814-8152
β-strand81618
α-helix8171
Chain B: 24 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix3-2119
α-helix25-262
α-helix27-348
α-helix39-468
α-helix60-623
α-helix65-8521
α-helix89-11527
α-helix120-1234
α-helix129-1313
α-helix136-1416
α-helix145-1484
α-helix149-1535
α-helix159-1646
α-helix174-19926
α-helix2011
α-helix204-22623
α-helix227-2293
α-helix235-2384
α-helix251-2588
α-helix262-2698
α-helix273-2753
α-helix284-30118
α-helix307-33226
α-helix338-3403
Chain C: 10 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix17-3822
α-helix42-443
α-helix47-537
α-helix56-9035
α-helix96-994
α-helix101-12222
α-helix136-17439
α-helix178-20528
α-helix206-2083
α-helix209-2124
Chain D: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix16-4732
α-helix53-553
α-helix57-593
α-helix61-8323
α-helix92-12736
α-helix134-16229
Chain E: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-4234
α-helix47-493
α-helix55-7521
α-helix84-12138
α-helix123-1253
α-helix126-15126
Chain F: 7 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-4234
α-helix47-493
α-helix50-534
α-helix55-7521
α-helix84-11936
α-helix123-1253
α-helix126-15328
Chain G: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-4335
α-helix47-493
α-helix50-534
α-helix55-7521
α-helix84-11936
α-helix125-15228
Chain H: 6 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand213
β-strand513
α-helix9-4335
α-helix47-493
α-helix55-617
α-helix63-7513
α-helix84-12138
α-helix125-15329

8 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
Nanobody 2WVA149Qprotein142Lama glama
Sequence of entity 1 (D), FASTA
>9MJ4_1 V-type proton ATPase subunit c' (chains D)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE
Sequence of entity 2 (C), FASTA
>9MJ4_2 V-type proton ATPase subunit c'' (chains C)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ
Sequence of entity 3 (N), FASTA
>9MJ4_3 V0 assembly protein 1 (chains N)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN
Sequence of entity 4 (M), FASTA
>9MJ4_4 V-type proton ATPase subunit e (chains M)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE
Sequence of entity 5 (E, F, G, H, I, J, K, L), FASTA
>9MJ4_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
>9MJ4_6 Yeast V-ATPase subunit f (chains O)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR
Sequence of entity 7 (B), FASTA
>9MJ4_7 V-type proton ATPase subunit d (chains B)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY
Sequence of entity 8 (A), FASTA
>9MJ4_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
Sequence of entity 9 (Q), FASTA
>9MJ4_9 Nanobody 2WVA149 (chains Q)
QVQLQESGGGLVQAGGSLRLSCAVSGSIFSGNAMDWYRQAPGKQRELVASLTSTGSTNYA
DSVKGRFTITRDNAKNTVYLQMNSLKPEDTAVYYCHALIYRSRLDLAPGNYWGQGTQVTV
SSAAAYPYDVPDYGSHHHHHHX

Primary citation

Monoclonal nanobodies alter the activity and assembly of the yeast vacuolar H + -ATPase. Knight, K., Park, J.B., Oot, R.A. et al. bioRxiv (2025). DOI 10.1101/2025.01.10.632502 · 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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