7FDC: Reconstituted V-ATPase, state3

CryoEM Structures of Reconstituted V-ATPase, state3. Determined by electron microscopy at 6.6 Å resolution. Released 22 Dec 2021.

Method: Electron microscopy
Resolution: 6.6 Å
Organisms: Saccharomyces cerevisiae S288C, Homo sapiens
Chains: 31
Atoms: 64,497
Mol. weight: 991.83 kDa
Released: 22 Dec 2021

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

Secondary structure: helices and β-sheets

7FDC contains 360 α-helices and 233 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-43	34
α-helix	50-53	4
α-helix	55-77	23
α-helix	84-119	36
α-helix	126-155	30

Chain A: 22 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	24-30	7	1
β-strand	35-38	4	1
β-strand	48-51	4	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	84-87	4	1
β-strand	93-96	4	2
β-strand	104-105	2	3
β-strand	111	1	3
α-helix	112-119	8
β-strand	123	1	4
β-strand	139-143	5	5
β-strand	151-152	2	6
β-strand	157-161	5	5
β-strand	170-173	4	5
α-helix	174-175	2
β-strand	180-182	3	6
β-strand	189-191	3	5
β-strand	198-201	4	6
β-strand	207-209	3	6
β-strand	213-216	4	2
α-helix	220-221	2
β-strand	225-226	2	3
β-strand	232	1	7
α-helix	238	1
α-helix	239-243	5
β-strand	247	1	7
β-strand	253	1	8
α-helix	264-272	9
β-strand	277-285	9	3
α-helix	288-296	9
β-strand	302-303	2	9
β-strand	307-308	2	9
α-helix	312-314	3
β-strand	315-321	7	3
α-helix	326-344	19
β-strand	349-353	5	3
α-helix	357-371	15
α-helix	384-392	9
β-strand	396-399	4	3
β-strand	407-410	4	3
β-strand	413	1	3
β-strand	414	1	8
α-helix	426-434	9
β-strand	437-438	2	8
α-helix	443-447	5
β-strand	460-461	2	8
α-helix	462-464	3
α-helix	468-474	7
α-helix	478-502	25
α-helix	509-524	16
α-helix	540-561	22
α-helix	567-574	8
α-helix	577-582	6
α-helix	583-586	4
α-helix	595-615	21

Chain b: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	9-43	35
α-helix	47-49	3
α-helix	52-54	3
α-helix	55-75	21
α-helix	84-119	36
α-helix	123-125	3
α-helix	126-136	11
α-helix	138-156	19

Chain B: 21 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	16-18	3
β-strand	27-28	2	1
β-strand	31-35	5	1
β-strand	38-42	5	1
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	92-95	4	1
β-strand	101-104	4	10
β-strand	112-113	2	11
β-strand	119	1	11
β-strand	130-133	4	10
α-helix	138	1
β-strand	139	1	4
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	12
β-strand	150-151	2	13
β-strand	152	1	14
α-helix	156-161	6
β-strand	164-165	2	13
β-strand	169	1	11
β-strand	172-175	4	15
α-helix	180-189	10
β-strand	192	1	14
β-strand	209-217	9	11
α-helix	220-232	13
α-helix	234-237	4
β-strand	238-244	7	11
α-helix	250-253	4
α-helix	255-270	16
β-strand	274-278	5	11
α-helix	282-290	9
α-helix	301-303	3
α-helix	308-316	9
β-strand	320	1	11
β-strand	321-322	2	12
β-strand	329-333	5	11
β-strand	334-337	4	15
α-helix	345-353	9
β-strand	358-359	2	15
β-strand	360	1	16
α-helix	362-366	5
β-strand	373	1	16
α-helix	395-420	26
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	478-483	6

Chain c: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	9-45	37
α-helix	47-49	3
α-helix	55-62	8
α-helix	63-65	3
α-helix	66-77	12
α-helix	84-86	3
α-helix	89-119	31
α-helix	123-125	3
α-helix	130-156	27

Chain C: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-37	4	1
β-strand	48-51	4	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	84-86	3	1
β-strand	93-96	4	17
α-helix	113-119	7
β-strand	123	1	18
α-helix	124-125	2
β-strand	138-143	6	19
β-strand	151-153	3	20
β-strand	157-161	5	19
β-strand	172-173	2	19
α-helix	174-175	2
β-strand	179-185	7	20
β-strand	189-192	4	19
β-strand	196	1	21
β-strand	198-201	4	20
β-strand	205	1	20
β-strand	210	1	21
β-strand	213-216	4	17
α-helix	220-222	3
β-strand	226-227	2	22
β-strand	232-233	2	23
α-helix	238-243	6
β-strand	246-247	2	23
β-strand	251-255	5	22
α-helix	262-272	11
β-strand	278-285	8	22
α-helix	288-296	9
β-strand	315-321	7	22
α-helix	326-345	20
β-strand	349-356	8	22
α-helix	357-370	14
α-helix	373-375	3
α-helix	377-379	3
α-helix	384-393	10
β-strand	396-398	3	22
β-strand	409-416	8	22
α-helix	419-421	3
α-helix	426-434	9
β-strand	437-438	2	22
α-helix	443-447	5
β-strand	460	1	22
α-helix	464-474	11
α-helix	477-502	26
α-helix	509-521	13
α-helix	522-526	5
α-helix	540-563	24
α-helix	567-574	8
α-helix	576-582	7
α-helix	584-586	3
α-helix	595-614	20

Chain d: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	4-23	20
α-helix	31-34	4
α-helix	37-39	3
α-helix	40-46	7
α-helix	59-61	3

Chain D: 21 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
β-strand	27-28	2	1
β-strand	33-35	3	1
β-strand	38-40	3	1
β-strand	52-56	5	1
β-strand	62-70	9	1
β-strand	75-79	5	1
β-strand	92-95	4	1
β-strand	101-104	4	24
α-helix	106-108	3
β-strand	112-113	2	25
β-strand	119	1	25
β-strand	130-133	4	24
β-strand	139	1	18
α-helix	141-143	3
β-strand	144-145	2	26
β-strand	150-152	3	27
α-helix	156-161	6
β-strand	164-165	2	27
β-strand	172-175	4	28
α-helix	181-189	9
β-strand	192-193	2	27
β-strand	208-217	10	25
α-helix	219-231	13
α-helix	234-237	4
β-strand	238-244	7	25
α-helix	249-253	5
α-helix	255-270	16
β-strand	273-279	7	25
α-helix	281-293	13
β-strand	299-301	3	29
β-strand	304-305	2	29
α-helix	308-316	9
β-strand	321-322	2	26
β-strand	328-333	6	25
β-strand	334-337	4	28
α-helix	345-353	9
β-strand	357	1	30
β-strand	359	1	28
β-strand	360	1	31
α-helix	362-366	5
β-strand	373	1	31
β-strand	379	1	30
α-helix	383-386	4
α-helix	397-420	24
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-466	13
α-helix	470-472	3
α-helix	478-480	3
α-helix	481-485	5

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Yeast Vacuolar ATPase A subunit	A, C, E	protein	617	Saccharomyces cerevisiae S288C	P17255 (AlphaFold model)
V-type proton ATPase subunit B	B, D, F	protein	517	Saccharomyces cerevisiae S288C	P16140 (AlphaFold model)
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae S288C	P22203 (AlphaFold model)
V-type proton ATPase subunit G	H, J, L	protein	122	Saccharomyces cerevisiae S288C	P48836 (AlphaFold model)
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae S288C	P32610
V-type proton ATPase subunit F	N	protein	118	Saccharomyces cerevisiae S288C	P39111
V-type proton ATPase subunit C	O	protein	392	Saccharomyces cerevisiae S288C	P31412
Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)	P	protein	469	Saccharomyces cerevisiae S288C, Homo sapiens	P41807, Q9UI12
Yeast Vacuolar ATPase a subunit	Q	protein	840	Saccharomyces cerevisiae S288C	P32563
V-type proton ATPase subunit d	S	protein	345	Saccharomyces cerevisiae S288C	P32366
V-type proton ATPase subunit c''	T	protein	213	Saccharomyces cerevisiae S288C	P23968
V-type proton ATPase subunit c'	U	protein	164	Saccharomyces cerevisiae S288C	P32842

4 more molecules are not listed.

Sequence of entity 1 (A, C, E), FASTA

>7FDC_1 Yeast Vacuolar ATPase A subunit (chains A, C, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTD

Sequence of entity 2 (B, D, F), FASTA

>7FDC_2 V-type proton ATPase subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Sequence of entity 3 (G, I, K), FASTA

>7FDC_3 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 4 (H, J, L), FASTA

>7FDC_4 V-type proton ATPase subunit G (chains H, J, L)
MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDK
ELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHIN
AL

Sequence of entity 5 (M), FASTA

>7FDC_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 6 (N), FASTA

>7FDC_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 7 (O), FASTA

>7FDC_7 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 8 (P), FASTA

>7FDC_8 Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYS
SELKSGRLEWSPVHKSEKFWRENAVRLNEKNYELLKILTKLLEVSDDPQVLAVAAHDVGE
YVRHYPRGKRVIEQLGGKQLVMNHMHHEDQQVRYNALLAVQKLMVHNWE

Sequence of entity 9 (Q), FASTA

>7FDC_9 Yeast Vacuolar ATPase a subunit (chains Q)
MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEER
LIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAI
GASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFS
HGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELY
AIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARL
GIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFA
IMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYN
DIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLS
ILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVK
DGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTH
KKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTI
EFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFAL
TCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

Sequence of entity 10 (S), FASTA

>7FDC_10 V-type proton ATPase subunit d (chains S)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 11 (T), FASTA

>7FDC_11 V-type proton ATPase subunit c'' (chains T)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 12 (U), FASTA

>7FDC_12 V-type proton ATPase subunit c' (chains U)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Primary citation

CryoEM Structures of Reconstituted V-ATPase and Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Khan, M.M., Lee, S., Oot, R.A. et al. EMBO J (2021).

Other PDB entries of the same protein (UniProt P17255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GPP 1.35 Å, Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I
1DFA 2.0 Å, Crystal structure of pi-scei in C2 space group
1EF0 2.1 Å, Crystal structure of pi-scei miniprecursor
1JVA 2.1 Å, Crystal structure of the VMA1-derived endonuclease bearing the N and C extein propeptides
1VDE 2.4 Å, Pi-scei, a homing endonuclease with protein splicing activity
9COP 2.7 Å, Yeast RAVE bound to V-ATPase V1 complex
1UM2 2.9 Å, Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment
1LWT 3.2 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA…
7TMO 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1
7TMP 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2
7TMQ 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 3
1LWS 3.5 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition…

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