7TMS: V-ATPase from Saccharomyces cerevisiae, State 2

V-ATPase from Saccharomyces cerevisiae, State 2. Determined by electron microscopy at 3.8 Å resolution. Released 13 Apr 2022.

Method
Electron microscopy
Resolution
3.8 Å
Organism
Saccharomyces cerevisiae
Chains
31
Atoms
57,652
Mol. weight
989.86 kDa
Ligands
ADP
Released
13 Apr 2022

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

Secondary structure: helices and β-sheets

7TMS contains 369 α-helices and 264 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: 37 helices, 14 β-strands

ElementResiduesLengthSheet
β-strand14-21869
α-helix26-3510
α-helix56-7823
α-helix86-9510
α-helix106-14338
β-strand187-191570
α-helix193-1953
α-helix196-20611
β-strand213-217570
β-strand222-224371
β-strand229-231371
β-strand234-238570
α-helix243-25513
β-strand260170
α-helix267-32458
β-strand335-342869
α-helix343-3453
α-helix346-36015
β-strand367-370469
α-helix376-3783
β-strand379172
α-helix388-39710
α-helix399-4013
α-helix408-42316
α-helix426-44116
α-helix443-4475
α-helix456-4594
α-helix462-47918
β-strand482173
β-strand485173
α-helix486-4872
β-strand506174
α-helix520-5223
α-helix528-56134
α-helix566-5672
α-helix568-5725
α-helix573-5797
α-helix580-5845
α-helix585-59511
α-helix598-6014
α-helix604-6074
α-helix611-6155
α-helix630-65021
α-helix711-73222
α-helix734-75421
α-helix764-78017
α-helix781-79010
α-helix791-7999
α-helix800-8056
α-helix806-8094
β-strand816172
Chain A: 27 helices, 39 β-strands
ElementResiduesLengthSheet
β-strand25-3171
β-strand34-3851
α-helix431
β-strand4412
β-strand48-5141
β-strand56-6491
β-strand67-7261
β-strand8013
β-strand85-8731
β-strand93-9644
β-strand104-10525
β-strand11115
α-helix112-1198
β-strand12316
α-helix137-1382
β-strand139-14357
β-strand151-15228
β-strand157-16157
β-strand170-17347
α-helix174-1752
β-strand180-18568
β-strand189-19137
β-strand196-20168
β-strand206-21058
β-strand213-21644
α-helix220-2223
β-strand223-22649
α-helix227-2293
β-strand232110
α-helix238-2425
β-strand247110
β-strand251-25555
α-helix262-27211
β-strand277-28595
α-helix287-29610
α-helix297-2993
β-strand301-302211
β-strand309-310211
α-helix311-3133
β-strand315-32175
α-helix326-34419
β-strand349-35465
α-helix357-37115
α-helix373-3742
β-strand375-377312
β-strand380-381212
α-helix384-39310
β-strand398-40039
β-strand407-40829
β-strand409-41685
α-helix426-4349
β-strand437-43825
β-strand441113
α-helix443-4475
β-strand454113
β-strand460-46125
α-helix468-4747
α-helix478-50225
α-helix504-5063
α-helix509-52113
α-helix522-5265
α-helix540-56223
α-helix567-5737
α-helix575-58410
α-helix589-5913
α-helix593-61422
Chain b: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix221-24424
α-helix251-2544
Chain B: 23 helices, 32 β-strands
ElementResiduesLengthSheet
β-strand26-2831
β-strand31-3551
β-strand38-4141
β-strand4813
β-strand52-5651
β-strand62-71101
β-strand74-7961
β-strand87114
β-strand92-9541
β-strand102-104315
α-helix106-1083
β-strand112-113216
β-strand119116
β-strand130-132315
α-helix1331
α-helix137-1382
β-strand13916
α-helix1401
β-strand144-145216
β-strand150-152317
α-helix156-1594
β-strand164-165217
β-strand169116
β-strand172-174316
α-helix180-19011
β-strand192-193217
β-strand208-214716
β-strand217118
α-helix219-23113
α-helix234-2374
β-strand238-241416
β-strand244118
α-helix249-26517
α-helix266-2705
β-strand273-279716
α-helix281-29414
α-helix297-2993
α-helix301-3033
α-helix308-3169
β-strand320-322316
β-strand328-336916
α-helix3371
α-helix345-3539
β-strand357119
β-strand358-359216
β-strand360120
α-helix362-3665
β-strand373120
β-strand379119
α-helix383-3853
α-helix396-41722
α-helix427-43812
α-helix439-4446
α-helix454-46512
α-helix478-4847
Chain c: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix17-3923
α-helix47-537
α-helix56-9237
α-helix96-12227
α-helix136-17641
α-helix178-20730
Chain C: 25 helices, 40 β-strands
ElementResiduesLengthSheet
β-strand25-3171
β-strand33-3861
β-strand44114
β-strand47-5151
β-strand56-6381
β-strand68-7251
β-strand80121
β-strand84-9181
β-strand93-96422
β-strand104-105223
α-helix112-1187
β-strand123124
α-helix137-1382
β-strand139-143525
β-strand151-152226
β-strand157-162625
β-strand170-173425
α-helix174-1752
β-strand180-185626
β-strand189-191325
β-strand198-201426
β-strand206-209426
β-strand213-216422
α-helix220-2223
β-strand223-226427
β-strand232128
α-helix238-2436
β-strand247128
β-strand251-255523
α-helix261-27111
β-strand277-285923
α-helix287-2937
α-helix297-2993
β-strand301-302229
β-strand309-310229
α-helix311-3133
β-strand315-321723
α-helix326-34419
β-strand349-354623
α-helix357-37115
α-helix373-3742
β-strand375-377330
β-strand380-381230
α-helix384-3929
β-strand398-400327
β-strand407-408227
β-strand409-416823
β-strand419131
β-strand422131
α-helix426-4327
β-strand437-438223
β-strand441132
α-helix443-4475
β-strand454132
β-strand460-461223
α-helix468-4747
α-helix478-50225
α-helix509-52113
α-helix522-5265
α-helix540-56223
α-helix567-5737
α-helix575-5839
α-helix584-5863
α-helix589-5913
α-helix593-61422
Chain d: 24 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix5-84
α-helix11-2212
α-helix25-262
α-helix27-348
α-helix39-479
α-helix52-554
α-helix65-8521
α-helix90-11122
α-helix121-1266
α-helix129-1313
α-helix136-1405
α-helix145-1528
α-helix159-1657
α-helix176-1816
α-helix182-19918
α-helix200-2012
α-helix204-22623
α-helix235-2417
α-helix253-2586
α-helix262-2698
α-helix273-2753
α-helix284-30118
α-helix307-33125
α-helix335-3406
Chain D: 24 helices, 33 β-strands
ElementResiduesLengthSheet
β-strand26-2831
β-strand31-3551
β-strand38-4141
β-strand48121
β-strand52-5651
α-helix571
β-strand62-71101
β-strand74-7961
β-strand87133
β-strand92-9541
β-strand101-104434
α-helix106-1083
β-strand112-114335
β-strand119135
β-strand130-133434
α-helix136-1383
β-strand139124
α-helix1401
α-helix141-1433
β-strand144-145236
β-strand150-151237
α-helix156-1594
β-strand164-165237
β-strand169135
β-strand172-174335
α-helix180-18910
β-strand193137
α-helix2081
β-strand209-217935
α-helix219-23113
α-helix235-2373
β-strand238-244735
α-helix250-2534
α-helix254-26815
β-strand273-279735
α-helix281-29414
β-strand299138
α-helix301-3033
β-strand305138
α-helix308-3169
β-strand320135
β-strand321-322236
β-strand328-336935
α-helix345-3539
β-strand357139
β-strand358-359235
β-strand360140
α-helix362-3665
β-strand373140
β-strand379139
α-helix383-3853
α-helix396-42025
α-helix427-43812
α-helix439-4435
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
>7TMS_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
>7TMS_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
>7TMS_3 V-ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD
Sequence of entity 4 (H, J, L), FASTA
>7TMS_4 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL
Sequence of entity 5 (M), FASTA
>7TMS_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF
Sequence of entity 6 (N), FASTA
>7TMS_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE
Sequence of entity 7 (O), FASTA
>7TMS_7 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL
Sequence of entity 8 (P), FASTA
>7TMS_8 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK
Sequence of entity 9 (a), FASTA
>7TMS_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
>7TMS_10 V0 assembly protein 1 (chains b)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN
Sequence of entity 11 (c), FASTA
>7TMS_11 V-type proton ATPase subunit c'' (chains c)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ
Sequence of entity 12 (d), FASTA
>7TMS_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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