7FDB: Reconstituted V-ATPase,State2

CryoEM Structures of Reconstituted V-ATPase,State2. Determined by electron microscopy at 4.8 Å resolution. Released 22 Dec 2021.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Saccharomyces cerevisiae S288C, Homo sapiens
Chains: 31
Atoms: 64,497
Mol. weight: 991.83 kDa
Released: 22 Dec 2021

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

Secondary structure: helices and β-sheets

7FDB contains 345 α-helices and 260 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	10-45	36
α-helix	55-77	23
α-helix	84-116	33
α-helix	123-125	3
α-helix	126-155	30

Chain A: 24 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-37	4	1
β-strand	44	1	2
β-strand	47-51	5	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	3
β-strand	84-91	8	1
β-strand	93-96	4	4
β-strand	104-105	2	5
β-strand	111	1	5
α-helix	112-119	8
β-strand	123	1	6
β-strand	138-142	5	7
β-strand	150-152	3	8
β-strand	157-161	5	7
β-strand	170-173	4	7
α-helix	174-175	2
β-strand	180-185	6	8
β-strand	189-192	4	7
β-strand	198-201	4	8
β-strand	207-209	3	8
β-strand	213-216	4	4
β-strand	225-227	3	5
β-strand	232-233	2	9
α-helix	234	1
α-helix	238-242	5
β-strand	246-247	2	9
β-strand	250	1	5
β-strand	252-255	4	10
α-helix	262-271	10
β-strand	278-285	8	5
α-helix	288-299	12
α-helix	312-314	3
β-strand	315-321	7	5
α-helix	328-345	18
β-strand	350-353	4	5
α-helix	357-371	15
α-helix	373-375	3
α-helix	377-379	3
α-helix	384-393	10
β-strand	396-399	4	5
β-strand	407-413	7	5
β-strand	414-416	3	10
α-helix	426-432	7
β-strand	437-441	5	10
α-helix	444-447	4
β-strand	454-460	7	10
α-helix	464-474	11
α-helix	479-502	24
α-helix	509-520	12
α-helix	521-525	5
α-helix	533-536	4
α-helix	540-562	23
α-helix	567-574	8
α-helix	577-584	8
α-helix	588	1
α-helix	595-615	21

Chain b: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	9-45	37
α-helix	55-75	21
α-helix	84-121	38
α-helix	123-125	3
α-helix	126-132	7
α-helix	134-156	23

Chain B: 27 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	11-16	6
α-helix	17-19	3
β-strand	26-28	3	1
β-strand	33-35	3	1
β-strand	38-40	3	1
α-helix	47	1
β-strand	48	1	3
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	103-104	2	11
α-helix	106-108	3
β-strand	112-114	3	12
β-strand	119	1	12
β-strand	130-131	2	11
α-helix	138	1
β-strand	139	1	6
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	13
α-helix	146-147	2
β-strand	148-151	4	14
α-helix	156-161	6
β-strand	164-166	3	14
β-strand	169	1	12
β-strand	172-174	3	15
α-helix	180-189	10
α-helix	206-208	3
β-strand	209-217	9	12
α-helix	219-232	14
α-helix	234-237	4
β-strand	238-244	7	12
α-helix	249-252	4
α-helix	254-270	17
β-strand	273-278	6	12
α-helix	281-295	15
α-helix	297-298	2
β-strand	299-301	3	16
β-strand	304-305	2	16
α-helix	308-316	9
β-strand	320	1	12
β-strand	321-322	2	13
β-strand	328-331	4	12
β-strand	334-336	3	15
α-helix	345-353	9
β-strand	357	1	17
β-strand	358-359	2	15
α-helix	363-366	4
β-strand	379	1	17
α-helix	383-386	4
α-helix	396-420	25
α-helix	422-424	3
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	478-484	7

Chain c: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	9-43	35
α-helix	47-49	3
α-helix	55-62	8
α-helix	63-65	3
α-helix	66-75	10
α-helix	89-121	33
α-helix	126-142	17
α-helix	144-155	12

Chain C: 22 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
β-strand	48-51	4	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	18
β-strand	84-87	4	1
β-strand	93-96	4	19
β-strand	104-105	2	20
β-strand	111	1	20
α-helix	112-119	8
β-strand	123	1	21
β-strand	139-143	5	22
β-strand	151-152	2	23
β-strand	157-161	5	22
β-strand	170-173	4	22
β-strand	180-185	6	23
α-helix	186-187	2
β-strand	189-191	3	22
β-strand	198-201	4	23
β-strand	207-209	3	23
β-strand	213-216	4	19
α-helix	220-222	3
β-strand	225-227	3	20
β-strand	232-233	2	24
α-helix	238	1
α-helix	239-243	5
β-strand	246-247	2	24
β-strand	251-253	3	20
α-helix	263-271	9
β-strand	277-281	5	20
α-helix	288-296	9
α-helix	297-299	3
β-strand	302	1	25
β-strand	308	1	25
β-strand	315-318	4	20
α-helix	326-345	20
β-strand	349-354	6	20
α-helix	358-371	14
β-strand	377	1	26
β-strand	380	1	26
α-helix	384-393	10
β-strand	396-399	4	20
α-helix	400	1
β-strand	407-413	7	20
α-helix	426-434	9
β-strand	437-438	2	20
β-strand	441	1	27
α-helix	443-447	5
β-strand	454	1	27
β-strand	460	1	20
α-helix	464-474	11
α-helix	478-502	25
α-helix	509-521	13
α-helix	522-526	5
α-helix	540-563	24
α-helix	567-574	8
α-helix	576-586	11
α-helix	595-615	21

Chain d: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-51	22
α-helix	59-62	4
β-strand	63	1	77

Chain D: 21 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	10-19	10
β-strand	28	1	1
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	18
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	28
β-strand	113	1	29
β-strand	119	1	29
β-strand	130-133	4	28
α-helix	138	1
β-strand	139	1	21
α-helix	140	1
α-helix	141-143	3
β-strand	145	1	30
β-strand	148	1	31
α-helix	156-159	4
β-strand	166	1	31
β-strand	169	1	32
β-strand	172-174	3	33
α-helix	180-190	11
β-strand	210-213	4	32
β-strand	217	1	34
α-helix	219-231	13
α-helix	234-236	3
β-strand	244	1	34
α-helix	250-269	20
β-strand	274-278	5	32
α-helix	282-290	9
α-helix	301-303	3
α-helix	308-316	9
β-strand	321	1	30
β-strand	329-333	5	32
β-strand	334-336	3	33
α-helix	345-353	9
β-strand	357	1	35
β-strand	358	1	33
β-strand	360	1	36
α-helix	362-367	6
β-strand	373	1	36
β-strand	379	1	35
α-helix	383-386	4
β-strand	389	1	37
β-strand	392	1	37
α-helix	396-420	25
α-helix	422-424	3
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-463	10
α-helix	478-485	8

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

>7FDB_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

>7FDB_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

>7FDB_3 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

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

>7FDB_4 V-type proton ATPase subunit G (chains H, J, L)
MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDK
ELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHIN
AL

Sequence of entity 5 (M), FASTA

>7FDB_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 6 (N), FASTA

>7FDB_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 7 (O), FASTA

>7FDB_7 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 8 (P), FASTA

>7FDB_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

>7FDB_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

>7FDB_10 V-type proton ATPase subunit d (chains S)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 11 (T), FASTA

>7FDB_11 V-type proton ATPase subunit c'' (chains T)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 12 (U), FASTA

>7FDB_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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