7TMT: V-ATPase from Saccharomyces cerevisiae, State 3

V-ATPase from Saccharomyces cerevisiae, State 3. Determined by electron microscopy at 3.8 Å resolution. Released 20 Apr 2022.

Method
Electron microscopy
Resolution
3.8 Å
Organism
Saccharomyces cerevisiae
Chains
31
Atoms
53,433
Mol. weight
989.86 kDa
Ligands
ADP
Released
20 Apr 2022

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

Secondary structure: helices and β-sheets

7TMT contains 362 α-helices and 300 β-strands across 31 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: 39 helices, 22 β-strands

ElementResiduesLengthSheet
β-strand8189
β-strand13190
β-strand16-20591
α-helix26-3611
β-strand40-41291
α-helix45-473
α-helix50-523
α-helix56-7823
α-helix85-9814
α-helix107-14135
β-strand187192
β-strand188-192593
α-helix193-1953
α-helix196-20611
β-strand212-214392
β-strand217193
β-strand222-223294
β-strand230-231294
β-strand233-235393
β-strand237-239392
α-helix243-25513
β-strand259-261393
α-helix267-32559
α-helix3331
β-strand336-340591
α-helix346-35914
β-strand367-370491
α-helix376-3772
β-strand378-379295
β-strand380190
α-helix388-3958
α-helix400-4023
β-strand406189
α-helix409-42315
α-helix426-44116
α-helix443-4486
α-helix455-4606
α-helix464-47815
β-strand494-495296
β-strand506-507297
β-strand509-510296
α-helix526-56136
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-helix628-64619
α-helix647-6515
α-helix712-73221
α-helix734-75825
α-helix764-78017
α-helix781-79010
α-helix791-80010
α-helix801-8055
α-helix806-8094
β-strand815-816295
α-helix8171
Chain A: 27 helices, 44 β-strands
ElementResiduesLengthSheet
β-strand25-3171
β-strand34-3851
β-strand47-5151
β-strand56-6491
β-strand67-7261
β-strand8012
β-strand84-9181
β-strand93-9643
β-strand104-10524
β-strand11114
α-helix114-1185
β-strand12315
β-strand139-14356
β-strand151-15227
β-strand159-16136
β-strand16418
β-strand16718
β-strand170-17236
β-strand180-18567
α-helix186-1872
β-strand189-19136
β-strand198-20257
β-strand205-20957
β-strand213-21643
α-helix220-2223
β-strand22519
β-strand232110
α-helix238-2425
β-strand247110
β-strand251-255511
α-helix262-27110
β-strand278-28254
β-strand285112
α-helix287-29610
α-helix297-2993
β-strand301113
β-strand310113
α-helix311-3133
β-strand315-31844
β-strand321112
α-helix326-3305
α-helix332-34514
β-strand351-352211
β-strand353-35534
α-helix357-37115
α-helix373-3753
β-strand377114
β-strand380114
α-helix384-39310
β-strand398-39929
α-helix4001
β-strand407-40829
β-strand411-416611
α-helix426-4349
β-strand437115
β-strand438111
β-strand441116
α-helix443-4475
β-strand454116
β-strand461115
α-helix468-4747
α-helix478-50124
α-helix504-5063
α-helix509-52113
α-helix522-5265
α-helix540-56223
α-helix567-5737
α-helix575-5839
α-helix584-5863
α-helix589-5913
α-helix593-61523
Chain b: 2 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand215198
β-strand219198
α-helix221-24424
α-helix251-2544
Chain B: 25 helices, 33 β-strands
ElementResiduesLengthSheet
α-helix16-205
β-strand26-2831
β-strand31-3551
β-strand38-4141
β-strand4812
β-strand52-5651
α-helix571
β-strand62-71101
β-strand74-7961
β-strand92-9541
β-strand101-104417
β-strand113118
β-strand119118
β-strand130-133417
α-helix1381
β-strand13915
α-helix1401
α-helix141-1433
β-strand144119
β-strand150120
β-strand151-152221
α-helix156-1594
β-strand165120
β-strand169118
β-strand172-174322
α-helix180-19011
β-strand192-193221
α-helix195-1984
α-helix203-2053
β-strand210123
β-strand212-217618
α-helix219-23113
α-helix233-2375
β-strand238123
β-strand241-244418
α-helix249-26416
α-helix265-2695
β-strand274-279618
α-helix281-29414
α-helix297-2993
α-helix301-3033
α-helix308-3169
β-strand320-321218
β-strand322119
β-strand328-333618
β-strand334-336322
α-helix345-3539
β-strand356-357224
β-strand360122
α-helix362-3665
β-strand373122
β-strand379-380224
α-helix383-3864
α-helix396-41621
α-helix427-43812
α-helix439-4435
α-helix454-46512
α-helix478-4847
Chain c: 9 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix17-3721
α-helix42-509
α-helix56-9035
α-helix94-996
α-helix101-12424
α-helix131-1333
α-helix134-1385
α-helix139-17436
α-helix178-20831
Chain C: 25 helices, 45 β-strands
ElementResiduesLengthSheet
β-strand26-3051
β-strand34-3851
α-helix43-442
β-strand47125
β-strand4811
β-strand49-51325
β-strand56125
β-strand59-6461
β-strand67-7151
β-strand80126
β-strand85-91725
β-strand93127
β-strand96128
β-strand104-105229
β-strand111129
α-helix112-1187
β-strand123130
β-strand139-142431
β-strand151-152232
β-strand157133
β-strand160-161231
β-strand170131
β-strand173133
β-strand180-185632
β-strand189-191331
β-strand196-201632
β-strand202134
β-strand205134
β-strand208-210332
β-strand213128
β-strand216127
α-helix220-2223
β-strand225-226235
β-strand232136
α-helix238-2425
β-strand247136
α-helix262-27110
β-strand278-285829
α-helix287-29610
α-helix297-2993
α-helix311-3144
β-strand315-321729
α-helix326-34419
β-strand351-352229
β-strand355129
α-helix357-37115
α-helix373-3753
β-strand377137
β-strand380137
α-helix384-3929
β-strand397-399335
α-helix4051
β-strand407-409335
β-strand411-412229
α-helix426-4327
β-strand437-438238
β-strand441139
α-helix443-4475
β-strand454139
β-strand460-461238
α-helix468-4747
α-helix478-49922
α-helix504-5063
α-helix509-52416
α-helix540-56223
α-helix567-5737
α-helix575-5839
α-helix584-5863
α-helix589-5913
α-helix593-61523
Chain d: 20 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix6-2116
α-helix27-359
α-helix39-4810
α-helix53-564
α-helix65-8521
α-helix90-11122
α-helix121-1266
α-helix129-1313
α-helix136-1416
α-helix145-1539
α-helix159-1646
α-helix176-1805
α-helix181-19919
α-helix204-22724
α-helix235-2417
α-helix251-2588
α-helix262-2698
α-helix284-30118
α-helix307-33125
α-helix338-3403
Chain D: 24 helices, 37 β-strands
ElementResiduesLengthSheet
α-helix17-193
α-helix24-252
β-strand26-2721
β-strand31-3551
β-strand38-4251
β-strand48126
β-strand51-5661
β-strand62-71101
β-strand74-7961
β-strand87140
β-strand92-9981
β-strand101-104441
β-strand113-114242
β-strand119142
β-strand130-133441
β-strand139130
β-strand144143
β-strand150144
β-strand151145
α-helix156-1594
α-helix163-1642
β-strand165144
β-strand169146
β-strand172-174347
α-helix180-19011
β-strand193145
α-helix201-2044
β-strand213-214248
β-strand215-217349
α-helix219-23214
α-helix234-2374
β-strand241-242242
β-strand243-244249
α-helix251-2533
α-helix255-26410
α-helix265-2695
β-strand273-276446
β-strand278-279248
α-helix281-29414
α-helix297-2982
β-strand299150
β-strand305150
α-helix308-3169
β-strand322143
β-strand325143
β-strand328-331446
β-strand335-336247
α-helix338-3403
α-helix345-3539
β-strand357151
β-strand358-360347
α-helix362-3665
β-strand373147
β-strand379151
α-helix383-3853
α-helix396-41924
α-helix422-4243
α-helix427-44216
α-helix454-46512
α-helix470-4723
α-helix478-4847

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
H(+)-transporting two-sector ATPaseA, C, Eprotein617Saccharomyces cerevisiaeB3LH69 (AlphaFold model)
Vacuolar proton pump subunit BB, D, Fprotein517Saccharomyces cerevisiaeA0A6A5Q585
V-ATPase subunit EG, I, Kprotein233Saccharomyces cerevisiaeA0A6A5Q7Y8
V-type proton ATPase subunit GH, J, Lprotein114Saccharomyces cerevisiaeP48836 (AlphaFold model)
V-type proton ATPase subunit DMprotein256Saccharomyces cerevisiaeA0A6A5Q1W2
V-type proton ATPase subunit FNprotein118Saccharomyces cerevisiaeA0A6A5PYF6
V-type proton ATPase subunit COprotein392Saccharomyces cerevisiaeA0A6A5PTP1
V-type proton ATPase subunit HPprotein478Saccharomyces cerevisiaeP41807
V-type proton ATPase subunit a, vacuolar isoformaprotein840Saccharomyces cerevisiaeP32563
V0 assembly protein 1bprotein265Saccharomyces cerevisiaeP53262
V-type proton ATPase subunit c''cprotein213Saccharomyces cerevisiaeP23968
V-type proton ATPase subunit ddprotein345Saccharomyces cerevisiaeP32366

4 more molecules are not listed.

Sequence of entity 1 (A, C, E), FASTA
>7TMT_1 H(+)-transporting two-sector ATPase (chains A, C, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTD
Sequence of entity 2 (B, D, F), FASTA
>7TMT_2 Vacuolar proton pump subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI
Sequence of entity 3 (G, I, K), FASTA
>7TMT_3 V-ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD
Sequence of entity 4 (H, J, L), FASTA
>7TMT_4 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL
Sequence of entity 5 (M), FASTA
>7TMT_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF
Sequence of entity 6 (N), FASTA
>7TMT_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE
Sequence of entity 7 (O), FASTA
>7TMT_7 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL
Sequence of entity 8 (P), FASTA
>7TMT_8 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK
Sequence of entity 9 (a), FASTA
>7TMT_9 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 10 (b), FASTA
>7TMT_10 V0 assembly protein 1 (chains b)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN
Sequence of entity 11 (c), FASTA
>7TMT_11 V-type proton ATPase subunit c'' (chains c)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ
Sequence of entity 12 (d), FASTA
>7TMT_12 V-type proton ATPase subunit d (chains d)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P21

Primary citation

Coordinated conformational changes in the V 1 complex during V-ATPase reversible dissociation. Vasanthakumar, T., Keon, K.A., Bueler, S.A. et al. Nat Struct Mol Biol (2022) 29:430-439. DOI 10.1038/s41594-022-00757-z · PubMed

Other PDB entries of the same protein (UniProt B3LH69 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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