7TMR: V-ATPase from Saccharomyces cerevisiae, State 1

V-ATPase from Saccharomyces cerevisiae, State 1. Determined by electron microscopy at 3.5 Å resolution. Released 13 Apr 2022.

Method
Electron microscopy
Resolution
3.5 Å
Organism
Saccharomyces cerevisiae
Chains
31
Atoms
57,795
Mol. weight
989.86 kDa
Ligands
ADP
Released
13 Apr 2022

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

Secondary structure: helices and β-sheets

7TMR contains 361 α-helices and 257 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: 36 helices, 20 β-strands

ElementResiduesLengthSheet
β-strand14-20764
α-helix26-3611
β-strand40164
α-helix50-523
α-helix56-7823
α-helix86-949
α-helix107-14135
β-strand187165
β-strand189-191366
α-helix196-20611
β-strand212-213265
β-strand217166
β-strand222-223267
β-strand230-231267
β-strand234-235266
β-strand238-239265
α-helix243-25513
β-strand259-260266
α-helix267-30337
α-helix306-32520
β-strand336-342764
α-helix343-3453
α-helix346-35914
β-strand368-370364
α-helix376-3772
β-strand379168
α-helix385-39511
α-helix408-42114
α-helix426-44015
α-helix443-4475
α-helix456-4605
α-helix464-47815
β-strand481-482269
β-strand485-486269
β-strand494-495270
β-strand506171
β-strand509-510270
α-helix520-5223
α-helix526-56136
α-helix565-5673
α-helix568-5725
α-helix573-5797
α-helix580-5845
α-helix585-59511
α-helix598-6014
α-helix604-6074
α-helix608-61710
α-helix630-65021
α-helix712-73221
α-helix734-75825
α-helix764-77916
α-helix780-78910
α-helix790-79910
α-helix800-8056
α-helix806-8094
β-strand816168
Chain A: 26 helices, 37 β-strands
ElementResiduesLengthSheet
β-strand26-3161
β-strand34-3851
β-strand48-5141
β-strand56-6491
β-strand67-7261
β-strand8012
β-strand85-8731
β-strand93-9643
β-strand104-10524
α-helix112-1198
β-strand12315
α-helix124-1252
α-helix137-1382
β-strand139-14356
β-strand151-15227
β-strand157-16156
β-strand170-17346
β-strand180-18567
β-strand189-19136
β-strand196-20277
β-strand205-21067
β-strand213-21643
α-helix220-2223
β-strand223-22648
β-strand23219
α-helix238-2425
β-strand24719
β-strand251-25554
α-helix262-27110
β-strand277-28154
α-helix287-29610
β-strand301110
α-helix304-3074
β-strand310110
α-helix311-3144
β-strand315-31844
α-helix326-34419
β-strand349-35464
α-helix357-37115
α-helix373-3753
β-strand377111
β-strand380111
α-helix384-39310
β-strand398-40038
β-strand407-40828
β-strand409-41684
α-helix426-4349
β-strand437-43824
β-strand441112
α-helix443-4475
β-strand454112
β-strand460-46124
α-helix468-4747
α-helix478-50225
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-helix593-61422
Chain b: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix221-24424
α-helix251-2533
Chain B: 25 helices, 29 β-strands
ElementResiduesLengthSheet
α-helix17-204
β-strand27-2821
β-strand31-3551
β-strand38-4141
β-strand4812
β-strand52-5651
β-strand62-71101
β-strand74-7961
β-strand92-9541
β-strand101-104413
α-helix106-1083
β-strand112-113214
β-strand119114
β-strand130-133413
α-helix1381
β-strand13915
α-helix1401
α-helix141-1433
β-strand144115
β-strand150-152316
α-helix156-1594
α-helix1631
β-strand164-165216
β-strand169114
β-strand172-174317
α-helix180-19011
β-strand192-193216
α-helix195-1984
β-strand208-214714
β-strand217118
α-helix219-23012
α-helix234-2374
β-strand238-241414
β-strand244118
α-helix249-26921
β-strand273-279714
α-helix281-29414
α-helix301-3033
α-helix308-3169
β-strand322115
β-strand328-333614
β-strand334-336317
α-helix345-3539
β-strand357-360417
α-helix362-3665
β-strand373-379717
α-helix383-3864
α-helix396-42025
α-helix422-4243
α-helix427-43812
α-helix439-4435
α-helix454-46512
α-helix470-4723
α-helix478-4847
Chain c: 9 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix17-3923
α-helix42-443
α-helix47-537
α-helix56-9035
α-helix96-12328
α-helix132-1343
α-helix136-17641
α-helix178-20730
α-helix209-2113
Chain C: 24 helices, 34 β-strands
ElementResiduesLengthSheet
β-strand26-3161
β-strand34-3851
β-strand47-5151
β-strand56-6491
β-strand67-7261
β-strand85-9171
β-strand93-96419
β-strand104-105220
α-helix112-1198
α-helix124-1252
β-strand139-143521
β-strand151-152222
β-strand157-162621
β-strand170-173421
β-strand180-185622
β-strand189-191321
β-strand198-202522
β-strand205-209522
β-strand213-216419
α-helix220-2223
β-strand225-226220
α-helix227-2293
β-strand232123
α-helix238-2425
β-strand247123
β-strand252-254320
α-helix263-27210
β-strand277-285920
α-helix287-29610
α-helix297-2993
β-strand301-303324
β-strand308-310324
α-helix311-3144
β-strand315-321720
α-helix326-34419
β-strand349-355720
α-helix357-37115
β-strand376125
β-strand380125
α-helix384-39310
β-strand396-399420
β-strand407-415920
α-helix426-4349
β-strand437-438220
β-strand441126
α-helix443-4475
β-strand454126
β-strand460-461220
α-helix462-4643
α-helix468-4747
α-helix478-49922
α-helix509-52416
α-helix540-56223
α-helix567-5737
α-helix575-5839
α-helix584-5863
α-helix589-5913
α-helix593-61523
Chain d: 24 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix4-63
α-helix7-2115
α-helix25-262
α-helix27-348
α-helix39-479
α-helix52-554
α-helix65-8521
α-helix90-11122
α-helix122-1265
α-helix129-1313
α-helix136-1416
α-helix145-1539
α-helix159-1657
α-helix170-1723
α-helix176-1816
α-helix182-19817
α-helix204-22724
α-helix235-2417
α-helix251-2588
α-helix262-2698
α-helix273-2753
α-helix284-30118
α-helix307-33125
α-helix335-3406
Chain D: 22 helices, 32 β-strands
ElementResiduesLengthSheet
α-helix16-194
β-strand26-28327
β-strand31-35527
β-strand38-41427
β-strand51-56627
β-strand62-711027
β-strand74-79627
β-strand87128
β-strand92-99827
β-strand101-104429
α-helix106-1083
β-strand112-114330
β-strand119130
β-strand130-133429
α-helix138-1403
α-helix141-1433
β-strand144131
β-strand150-151232
α-helix156-1594
α-helix1631
β-strand164-165232
β-strand169130
β-strand172-174333
α-helix180-19011
β-strand193132
β-strand199134
β-strand202134
β-strand209-217930
α-helix219-23214
α-helix234-2374
β-strand238-244730
α-helix250-2534
α-helix255-26814
β-strand273-278630
α-helix281-29414
α-helix297-2982
β-strand299-301335
β-strand304-305235
α-helix308-31710
β-strand322131
β-strand328-333630
β-strand334-336333
α-helix345-3539
β-strand356-360533
α-helix362-3665
β-strand373-380833
β-strand388136
β-strand391136
α-helix396-41924
α-helix427-43812
α-helix439-4446
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 cerevisiaeP17255 (AlphaFold model)
Vacuolar proton pump subunit BB, D, Fprotein517Saccharomyces cerevisiaeP16140 (AlphaFold model)
V-type proton ATPase subunit EG, I, Kprotein233Saccharomyces cerevisiaeP22203 (AlphaFold model)
V-type proton ATPase subunit GH, J, Lprotein114Saccharomyces cerevisiaeP48836 (AlphaFold model)
V-type proton ATPase subunit DMprotein256Saccharomyces cerevisiaeP32610
V-type proton ATPase subunit FNprotein118Saccharomyces cerevisiaeP39111
V-type proton ATPase subunit COprotein392Saccharomyces cerevisiaeP31412
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
>7TMR_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
>7TMR_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
>7TMR_3 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD
Sequence of entity 4 (H, J, L), FASTA
>7TMR_4 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL
Sequence of entity 5 (M), FASTA
>7TMR_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF
Sequence of entity 6 (N), FASTA
>7TMR_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE
Sequence of entity 7 (O), FASTA
>7TMR_7 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL
Sequence of entity 8 (P), FASTA
>7TMR_8 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK
Sequence of entity 9 (a), FASTA
>7TMR_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
>7TMR_10 V0 assembly protein 1 (chains b)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN
Sequence of entity 11 (c), FASTA
>7TMR_11 V-type proton ATPase subunit c'' (chains c)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ
Sequence of entity 12 (d), FASTA
>7TMR_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 P17255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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