6O7X: V-type proton ATPase subunit C

Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3. Determined by electron microscopy at 8.7 Å resolution. Released 3 Apr 2019.

Method: Electron microscopy
Resolution: 8.7 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae (strain RM11-1a), Saccharomyces cerevisiae
Chains: 31
Atoms: 39,578
Mol. weight: 1003.72 kDa
Released: 3 Apr 2019

Explore 6O7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O7X contains 321 α-helices and 218 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: 33 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	51
α-helix	25-34	10
α-helix	59-77	19
α-helix	113-117	5
α-helix	119-162	44
β-strand	241-245	5	52
α-helix	246-248	3
α-helix	249-259	11
β-strand	267-270	4	52
β-strand	284-288	5	52
α-helix	297-304	8
β-strand	310-311	2	52
α-helix	321-351	31
α-helix	354-371	18
β-strand	380-384	5	51
α-helix	389-391	3
α-helix	392-405	14
β-strand	415	1	51
α-helix	457-468	12
α-helix	472-487	16
α-helix	489-493	5
α-helix	499-506	8
α-helix	508-524	17
β-strand	540-541	2	53
β-strand	552-553	2	54
β-strand	555-556	2	53
α-helix	566-568	3
α-helix	574-597	24
α-helix	599-607	9
α-helix	611-613	3
α-helix	614-618	5
α-helix	619-625	7
α-helix	629-641	13
α-helix	650-653	4
α-helix	655-663	9
α-helix	676-688	13
α-helix	690-702	13
α-helix	704-706	3
α-helix	768-790	23
α-helix	795-814	20
α-helix	827-843	17
α-helix	844-851	8
α-helix	853-865	13

Chain A: 27 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	8
β-strand	34-38	5	8
β-strand	47-51	5	8
β-strand	56-64	9	8
β-strand	67-72	6	8
α-helix	79	1
β-strand	80	1	22
β-strand	84-91	8	8
β-strand	94-96	3	23
β-strand	104-105	2	24
β-strand	111	1	24
α-helix	112-119	8
α-helix	124-125	2
β-strand	138-141	4	25
β-strand	142-143	2	26
β-strand	151-152	2	27
β-strand	157-160	4	26
β-strand	171-173	3	26
α-helix	174-175	2
β-strand	180-185	6	27
α-helix	186-187	2
β-strand	189-192	4	25
β-strand	196-202	7	27
β-strand	204-210	7	27
β-strand	213-215	3	23
β-strand	225-226	2	24
β-strand	231	1	28
α-helix	238-243	6
β-strand	248	1	28
β-strand	251-254	4	24
α-helix	262-272	11
β-strand	277-285	9	24
α-helix	288-296	9
α-helix	297-299	3
α-helix	301-302	2
α-helix	310-313	4
β-strand	315-321	7	24
α-helix	326-346	21
β-strand	349-355	7	24
α-helix	357-371	15
α-helix	384-394	11
β-strand	396-399	4	24
α-helix	400	1
β-strand	407-415	9	24
α-helix	426-434	9
β-strand	437-438	2	24
α-helix	443-449	7
α-helix	451	1
α-helix	453	1
β-strand	460-461	2	24
α-helix	464-474	11
α-helix	478-501	24
α-helix	509-521	13
α-helix	522-526	5
α-helix	540-562	23
α-helix	567-582	16
α-helix	584-586	3
α-helix	598-615	18

Chain b: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	223-245	23
α-helix	251-253	3

Chain B: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	8
β-strand	38-41	4	8
β-strand	48	1	22
β-strand	51-56	6	8
β-strand	62-71	10	8
β-strand	74-79	6	8
β-strand	92-99	8	8
β-strand	101-104	4	29
β-strand	111-114	4	30
β-strand	130-133	4	29
β-strand	150	1	31
α-helix	156-159	4
β-strand	165	1	31
β-strand	169	1	30
β-strand	172-175	4	32
α-helix	180-190	11
α-helix	194-201	8
β-strand	208-214	7	30
α-helix	219-232	14
β-strand	238-242	5	30
α-helix	249-269	21
β-strand	273-278	6	30
α-helix	281-290	10
α-helix	301-303	3
α-helix	308-317	10
β-strand	320-321	2	30
α-helix	322	1
β-strand	328-333	6	30
β-strand	334-337	4	32
α-helix	345-353	9
β-strand	356-360	5	32
α-helix	362-367	6
β-strand	373-380	8	32
α-helix	383-386	4
α-helix	396-419	24
α-helix	427-440	14
α-helix	454-465	12
α-helix	478-483	6

Chain c: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	18-38	21
α-helix	42-44	3
α-helix	47-53	7
α-helix	56-89	34
α-helix	94-96	3
α-helix	99-101	3
α-helix	102-122	21
α-helix	127-129	3
α-helix	136-176	41
α-helix	178-180	3
α-helix	181-191	11
α-helix	193-205	13

Chain C: 23 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	8
β-strand	34-38	5	8
β-strand	47-51	5	8
β-strand	56-64	9	8
β-strand	67-72	6	8
α-helix	79-80	2
β-strand	85-91	7	8
β-strand	93-96	4	33
β-strand	104-105	2	34
β-strand	111	1	34
α-helix	112-119	8
β-strand	138-141	4	35
β-strand	142-143	2	36
β-strand	151-153	3	37
β-strand	157-161	5	36
β-strand	170-173	4	36
α-helix	174-175	2
β-strand	179-185	7	37
β-strand	189-192	4	35
β-strand	196-201	6	37
β-strand	205-210	6	37
β-strand	213-216	4	33
α-helix	220-222	3
β-strand	225-227	3	34
β-strand	232-233	2	38
α-helix	238-243	6
β-strand	246-247	2	38
β-strand	252-255	4	34
α-helix	262-272	11
β-strand	277-282	6	34
β-strand	285	1	39
α-helix	288-296	9
α-helix	310-313	4
β-strand	315-318	4	34
β-strand	321	1	39
α-helix	326-346	21
β-strand	349-355	7	34
α-helix	358-371	14
α-helix	377-379	3
α-helix	383-393	11
β-strand	396-399	4	34
β-strand	407-416	10	34
α-helix	426-434	9
β-strand	437-439	3	34
α-helix	443-447	5
α-helix	456-458	3
β-strand	459-461	3	34
α-helix	464-474	11
α-helix	478-501	24
α-helix	509-526	18
α-helix	540-562	23
α-helix	567-574	8
α-helix	576-582	7
α-helix	583-585	3
β-strand	592	1	40
β-strand	596	1	40
α-helix	598-615	18

Chain d: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	6-8	3
α-helix	11-21	11
α-helix	27-34	8
α-helix	39-46	8
α-helix	65-85	21
α-helix	90-110	21
α-helix	137-140	4
α-helix	146-148	3
α-helix	149-153	5
α-helix	159-161	3
α-helix	174-199	26
α-helix	203-226	24
α-helix	235-238	4
α-helix	249-253	5
α-helix	254-257	4
α-helix	262-266	5
α-helix	284-297	14
α-helix	307-329	23

Chain D: 16 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	8
β-strand	38-41	4	8
α-helix	48	1
β-strand	51-56	6	8
β-strand	62-71	10	8
β-strand	74-79	6	8
β-strand	92-99	8	8
β-strand	101-104	4	41
β-strand	111-114	4	42
β-strand	119	1	42
β-strand	130-133	4	41
β-strand	150	1	43
α-helix	156-159	4
β-strand	165	1	43
β-strand	169	1	42
β-strand	172-174	3	44
α-helix	180-190	11
α-helix	195-201	7
β-strand	208-214	7	42
α-helix	219-232	14
β-strand	238-242	5	42
α-helix	249-269	21
β-strand	273-279	7	42
α-helix	281-293	13
β-strand	299	1	45
α-helix	301-303	3
β-strand	305	1	45
α-helix	308-317	10
β-strand	320-322	3	42
β-strand	327-333	7	42
β-strand	334-336	3	44
α-helix	345-353	9
β-strand	357	1	46
β-strand	358-359	2	44
β-strand	360	1	47
α-helix	362-367	6
β-strand	373	1	47
β-strand	379	1	46
α-helix	396-420	25
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	478-483	6

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
V-type proton ATPase subunit C	O	protein	392	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P31412 (AlphaFold model)
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32610 (AlphaFold model)
V-type proton ATPase subunit F	N	protein	118	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P39111 (AlphaFold model)
Vacuolar ATP synthase catalytic subunit A	A, C, E	protein	639	Saccharomyces cerevisiae (strain RM11-1a)	B3LH69 (AlphaFold model)
V-type proton ATPase subunit B	B, D, F	protein	517	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P16140
V-type proton ATPase subunit G	H, J, L	protein	114	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P48836
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22203
V-type proton ATPase subunit H	P	protein	478	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P41807
V-type proton ATPase subunit a, Golgi isoform	a	protein	890	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P37296
V0 assembly protein 1	b	protein	265	Saccharomyces cerevisiae	P53262
V-type proton ATPase subunit c''	c	protein	213	Saccharomyces cerevisiae	P23968
V-type proton ATPase subunit d	d	protein	345	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32366

4 more molecules are not listed.

Sequence of entity 1 (O), FASTA

>6O7X_1 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 2 (M), FASTA

>6O7X_2 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 3 (N), FASTA

>6O7X_3 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 4 (A, C, E), FASTA

>6O7X_4 Vacuolar ATP synthase catalytic subunit A (chains A, C, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTDDYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 5 (B, D, F), FASTA

>6O7X_5 V-type proton ATPase subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Sequence of entity 6 (H, J, L), FASTA

>6O7X_6 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 7 (G, I, K), FASTA

>6O7X_7 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 8 (P), FASTA

>6O7X_8 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Sequence of entity 9 (a), FASTA

>6O7X_9 V-type proton ATPase subunit a, Golgi isoform (chains a)
MNQEEAIFRSADMTYVQLYIPLEVIREVTFLLGKMSVFMVMDLNKDLTAFQRGYVNQLRR
FDEVERMVGFLNEVVEKHAAETWKYILHIDDEGNDIAQPDMADLINTMEPLSLENVNDMV
KEITDCESRARQLDESLDSLRSKLNDLLEQRQVIFECSKFIEVNPGIAGRATNPEIEQEE
RDVDEFRMTPDDISETLSDAFSFDDETPQDRGALGNDLTRNQSVEDLSFLEQGYQHRYMI
TGSIRRTKVDILNRILWRLLRGNLIFQNFPIEEPLLEGKEKVEKDCFIIFTHGETLLKKV
KRVIDSLNGKIVSLNTRSSELVDTLNRQIDDLQRILDTTEQTLHTELLVIHDQLPVWSAM
TKREKYVYTTLNKFQQESQGLIAEGWVPSTELIHLQDSLKDYIETLGSEYSTVFNVILTN
KLPPTYHRTNKFTQAFQSIVDAYGIATYKEINAGLATVVTFPFMFAIMFGDMGHGFILFL
MALFLVLNERKFGAMHRDEIFDMAFTGRYVLLLMGAFSVYTGLLYNDIFSKSMTIFKSGW
QWPSTFRKGESIEAKKTGVYPFGLDFAWHGTDNGLLFSNSYKMKLSILMGYAHMTYSFMF
SYINYRAKNSKVDIIGNFIPGLVFMQSIFGYLSWAIVYKWSKDWIKDDKPAPGLLNMLIN
MFLAPGTIDDQLYSGQAKLQVVLLLAALVCVPWLLLYKPLTLRRLNKNGGGGRPHGYQSV
GNIEHEEQIAQQRHSAEGFQGMIISDVASVADSINESVGGGEQGPFNFGDVMIHQVIHTI
EFCLNCISHTASYLRLWALSLAHAQLSSVLWDMTISNAFSSKNSGSPLAVMKVVFLFAMW
FVLTVCILVFMEGTSAMLHALRLHWVEAMSKFFEGEGYAYEPFSFRAIIE

Sequence of entity 10 (b), FASTA

>6O7X_10 V0 assembly protein 1 (chains b)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN

Sequence of entity 11 (c), FASTA

>6O7X_11 V-type proton ATPase subunit c'' (chains c)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 12 (d), FASTA

>6O7X_12 V-type proton ATPase subunit d (chains d)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Primary citation

Structural comparison of the vacuolar and Golgi V-ATPases fromSaccharomyces cerevisiae. Vasanthakumar, T., Bueler, S.A., Wu, D. et al. Proc Natl Acad Sci U S A (2019) 116:7272-7277. DOI 10.1073/pnas.1814818116 · PubMed

Other PDB entries of the same protein (UniProt P31412 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U7L 1.75 Å, Crystal Structure of subunit C (vma5p) of the yeast V-ATPase
4EFA 2.82 Å, Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast…
4DL0 2.9 Å, Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast…
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae
7TMR 3.5 Å, V-ATPase from Saccharomyces cerevisiae, State 1
9MOY 3.6 Å, Reconstituted yeast V-ATPase bound to Rtc5p
7FDE 3.8 Å, CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
9ODU 3.9 Å, Yeast V-ATPase bound to Rtc5p, rotary state 2
7FDA 4.2 Å, CryoEM Structure of Reconstituted V-ATPase, state1
7FDB 4.8 Å, CryoEM Structures of Reconstituted V-ATPase,State2
6O7V 6.6 Å, Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1
7FDC 6.6 Å, CryoEM Structures of Reconstituted V-ATPase, state3

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