5D80: Yeast V1-ATPase in the Autoinhibited Form

Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form. Determined by X-ray diffraction at 6.2 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 6.2 Å
Organism: Saccharomyces cerevisiae
Chains: 30
Atoms: 47,363
Mol. weight: 1189.53 kDa
Released: 8 Jun 2016

Explore 5D80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D80 contains 403 α-helices and 394 β-strands across 30 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: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	53
β-strand	35-39	5	53
β-strand	49-52	4	53
β-strand	57-65	9	53
β-strand	68-72	5	53
β-strand	81	1	54
β-strand	85-88	4	53
β-strand	94-97	4	55
β-strand	105-107	3	56
α-helix	113-119	7
β-strand	124	1	57
β-strand	140-143	4	58
β-strand	152-153	2	59
β-strand	158-162	5	58
α-helix	169-170	2
β-strand	171-174	4	58
α-helix	175-176	2
β-strand	181-186	6	59
β-strand	190-192	3	58
β-strand	199-203	5	59
β-strand	206-210	5	59
β-strand	214-217	4	55
α-helix	221-223	3
β-strand	226-227	2	56
α-helix	233-235	3
α-helix	239-243	5
β-strand	252-256	5	56
α-helix	263-272	10
β-strand	278-283	6	56
α-helix	288-297	10
β-strand	302	1	60
β-strand	311	1	60
β-strand	317-320	4	56
α-helix	328-331	4
α-helix	333-345	13
β-strand	350-356	7	56
α-helix	358-372	15
α-helix	374-376	3
α-helix	385-393	9
β-strand	397-400	4	56
β-strand	408-417	10	56
α-helix	427-435	9
β-strand	438-439	2	56
α-helix	444-447	4
β-strand	461-462	2	56
α-helix	465-472	8
α-helix	480-500	21
α-helix	510-521	12
α-helix	522-526	5
α-helix	541-562	22
α-helix	568-574	7
α-helix	576-582	7
α-helix	583-586	4
α-helix	595-611	17

Chain A: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	1
β-strand	35-39	5	1
β-strand	49-52	4	1
β-strand	57-65	9	1
β-strand	68-72	5	1
β-strand	81	1	2
β-strand	85-88	4	1
β-strand	94-97	4	3
β-strand	105-107	3	4
α-helix	113-119	7
β-strand	124	1	5
β-strand	140-143	4	6
β-strand	152-153	2	7
β-strand	158-162	5	6
α-helix	169-170	2
β-strand	171-174	4	6
α-helix	175-176	2
β-strand	181-186	6	7
β-strand	190-192	3	6
β-strand	199-203	5	7
β-strand	206-210	5	7
β-strand	214-217	4	3
α-helix	221-223	3
β-strand	224-227	4	4
α-helix	233-235	3
α-helix	239-243	5
β-strand	252-256	5	4
α-helix	263-272	10
β-strand	278-283	6	4
α-helix	288-297	10
β-strand	302	1	8
β-strand	311	1	8
β-strand	317-320	4	4
α-helix	328-331	4
α-helix	333-345	13
β-strand	350-356	7	4
α-helix	358-372	15
α-helix	374-376	3
α-helix	385-393	9
β-strand	397-401	5	4
β-strand	408-417	10	4
α-helix	427-435	9
β-strand	438-439	2	4
α-helix	444-447	4
β-strand	461-462	2	4
α-helix	465-472	8
α-helix	480-500	21
α-helix	510-521	12
α-helix	522-526	5
α-helix	541-562	22
α-helix	568-574	7
α-helix	576-582	7
α-helix	583-586	4
α-helix	595-611	17

Chains b and B: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	25-32	8	53
β-strand	35-39	5	53
β-strand	48-52	5	53
β-strand	57-65	9	53
β-strand	68-73	6	53
β-strand	81	1	61
β-strand	85-92	8	53
β-strand	94-97	4	62
β-strand	105-106	2	63
β-strand	112	1	63
α-helix	113-120	8
β-strand	140-143	4	64
α-helix	147-148	2
β-strand	152-154	3	65
β-strand	158-162	5	64
β-strand	171-174	4	64
α-helix	175-176	2
β-strand	180-186	7	65
α-helix	187-188	2
β-strand	190-192	3	64
β-strand	197-203	7	65
β-strand	206-211	6	65
β-strand	214-217	4	62
α-helix	221-223	3
β-strand	226-227	2	63
α-helix	233-235	3
α-helix	239-242	4
β-strand	252-254	3	63
α-helix	263-272	10
β-strand	279-286	8	63
α-helix	288-297	10
β-strand	302-303	2	66
β-strand	310-311	2	66
β-strand	316-322	7	63
α-helix	328-345	18
β-strand	350-356	7	63
α-helix	358-371	14
α-helix	374-376	3
α-helix	385-395	11
β-strand	397-400	4	63
α-helix	401	1
β-strand	408-415	8	63
α-helix	420-422	3
α-helix	427-435	9
β-strand	438-439	2	63
β-strand	461-462	2	63
α-helix	465-472	8
α-helix	479-502	24
α-helix	510-522	13
α-helix	523-527	5
α-helix	541-562	22
α-helix	568-571	4
α-helix	576-583	8
α-helix	594-615	22

Chains c and C: 21 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	25-32	8	53
β-strand	35-39	5	53
β-strand	48-52	5	53
β-strand	57-65	9	53
β-strand	68-73	6	53
β-strand	85-87	3	53
β-strand	94-97	4	67
β-strand	105-106	2	68
β-strand	112	1	68
α-helix	113-120	8
β-strand	124	1	69
β-strand	140-142	3	24
β-strand	152-154	3	70
β-strand	158	1	71
β-strand	174	1	71
α-helix	175-176	2
β-strand	180-186	7	70
β-strand	190-192	3	24
β-strand	197-203	7	70
β-strand	206-211	6	70
β-strand	214-217	4	67
α-helix	221-223	3
β-strand	224-227	4	68
β-strand	233	1	72
α-helix	239-243	5
β-strand	248	1	72
β-strand	252-254	3	68
α-helix	263-272	10
β-strand	278-286	9	68
α-helix	288-300	13
β-strand	307	1	20
β-strand	316-322	7	68
α-helix	328-346	19
β-strand	350-355	6	68
α-helix	358-371	14
α-helix	378-380	3
α-helix	385-393	9
β-strand	397-401	5	68
β-strand	408-415	8	68
α-helix	420-422	3
α-helix	427-433	7
β-strand	438-439	2	68
α-helix	444-447	4
β-strand	461-462	2	68
α-helix	465-472	8
α-helix	482-500	19
α-helix	510-522	13
α-helix	523-527	5
α-helix	541-562	22
α-helix	568-574	7
α-helix	577-583	7
α-helix	594-608	15

Chain d: 22 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	53
β-strand	38-41	4	53
β-strand	48	1	54
β-strand	52-56	5	53
β-strand	62-71	10	53
β-strand	75-79	5	53
β-strand	92-95	4	53
β-strand	101-104	4	73
β-strand	112-113	2	74
β-strand	119	1	74
α-helix	125-128	4
β-strand	130-133	4	73
α-helix	138	1
β-strand	139	1	57
α-helix	140	1
β-strand	144-145	2	75
β-strand	150-151	2	76
β-strand	164-165	2	76
β-strand	169	1	74
β-strand	172-174	3	77
α-helix	180-191	12
α-helix	207-208	2
β-strand	209-217	9	74
α-helix	219-232	14
β-strand	239-244	6	74
α-helix	249-264	16
α-helix	265-269	5
β-strand	274-279	6	74
α-helix	281-293	13
α-helix	297-299	3
α-helix	308-313	6
α-helix	316-318	3
β-strand	320	1	74
β-strand	321-322	2	75
β-strand	329-331	3	74
β-strand	334-336	3	77
α-helix	337	1
α-helix	338-340	3
α-helix	345-353	9
β-strand	358	1	77
α-helix	362-365	4
α-helix	381-384	4
α-helix	397-420	24
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	478-484	7

Chain D: 22 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	2
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	75-79	5	1
β-strand	92-95	4	1
β-strand	101-104	4	28
β-strand	112-113	2	29
β-strand	119	1	29
α-helix	125-128	4
β-strand	130-133	4	28
α-helix	138	1
β-strand	139	1	5
α-helix	140	1
β-strand	144-145	2	30
β-strand	150-151	2	31
β-strand	164-165	2	31
β-strand	169	1	29
β-strand	172-174	3	32
α-helix	180-191	12
α-helix	207-208	2
β-strand	209-217	9	29
α-helix	219-232	14
β-strand	239-244	6	29
α-helix	249-264	16
α-helix	265-269	5
β-strand	274-279	6	29
α-helix	281-293	13
α-helix	297-299	3
α-helix	308-313	6
α-helix	316-318	3
β-strand	320	1	29
β-strand	321-322	2	30
β-strand	329-331	3	29
β-strand	334-336	3	32
α-helix	337	1
α-helix	338-340	3
α-helix	345-353	9
β-strand	358	1	32
α-helix	362-365	4
α-helix	381-384	4
α-helix	396-420	25
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	478-484	7

Chains e and E: 20 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	53
β-strand	34	1	53
β-strand	39-42	4	53
α-helix	47	1
β-strand	48	1	61
β-strand	51-56	6	53
β-strand	62-71	10	53
β-strand	74-79	6	53
β-strand	92-99	8	53
β-strand	102-104	3	78
β-strand	112-114	3	79
β-strand	119	1	79
α-helix	125-128	4
β-strand	130-132	3	78
α-helix	138-140	3
β-strand	144-145	2	79
α-helix	146-147	2
β-strand	169	1	79
β-strand	172-175	4	80
α-helix	180-194	15
α-helix	195-197	3
β-strand	209-217	9	79
α-helix	219-232	14
β-strand	239-244	6	79
α-helix	249-264	16
α-helix	265-269	5
β-strand	273-279	7	79
α-helix	281-294	14
α-helix	301-303	3
α-helix	308-316	9
β-strand	320-322	3	79
β-strand	328-333	6	79
β-strand	334-337	4	80
α-helix	338-340	3
α-helix	345-353	9
β-strand	357	1	81
β-strand	358-359	2	80
β-strand	360	1	82
α-helix	362-365	4
β-strand	373	1	82
β-strand	379	1	81
α-helix	397-419	23
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	478-484	7

Chains f and F: 20 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	53
β-strand	33-35	3	53
β-strand	38-42	5	53
β-strand	51-56	6	53
β-strand	62-71	10	53
β-strand	74-79	6	53
β-strand	92-99	8	53
β-strand	101-102	2	83
β-strand	113-114	2	84
β-strand	119	1	84
α-helix	125-128	4
β-strand	132-133	2	83
α-helix	138	1
β-strand	139	1	69
α-helix	140	1
β-strand	144-145	2	85
β-strand	172-174	3	86
α-helix	180-189	10
β-strand	208-214	7	84
β-strand	217	1	87
α-helix	219-232	14
α-helix	235-237	3
β-strand	238-242	5	84
β-strand	244	1	87
α-helix	254-265	12
α-helix	266-270	5
β-strand	273-279	7	84
α-helix	281-294	14
α-helix	301-303	3
α-helix	308-316	9
β-strand	320	1	84
β-strand	321-322	2	85
β-strand	328-331	4	84
β-strand	334-336	3	86
α-helix	338-340	3
α-helix	345-353	9
β-strand	358-359	2	86
β-strand	360	1	88
α-helix	362-367	6
β-strand	373	1	88
α-helix	381-383	3
α-helix	396-419	24
α-helix	428-441	14
α-helix	454-464	11
α-helix	470-472	3
α-helix	478-481	4

15 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 catalytic subunit A	A, B, C, a, b, c	protein	617	Saccharomyces cerevisiae	P17255 (AlphaFold model)
V-type proton ATPase subunit B	D, E, F, d, e, f	protein	517	Saccharomyces cerevisiae	P16140 (AlphaFold model)
V-type proton ATPase subunit H	H, h	protein	478	Saccharomyces cerevisiae	P41807 (AlphaFold model)
V-type proton ATPase subunit G	J, L, N, j, l, n	protein	122	Saccharomyces cerevisiae	P48836 (AlphaFold model)
V-type proton ATPase subunit E	I, K, M, i, k, m	protein	233	Saccharomyces cerevisiae	P22203
V-type proton ATPase subunit D	G, g	protein	256	Saccharomyces cerevisiae	P32610
V-type proton ATPase subunit F	O, o	protein	118	Saccharomyces cerevisiae	P39111

Sequence of entity 1 (A, B, C, a, b, c), FASTA

>5D80_1 V-type proton ATPase catalytic subunit A (chains A, B, C, a, b, c)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTD

Sequence of entity 2 (D, E, F, d, e, f), FASTA

>5D80_2 V-type proton ATPase subunit B (chains D, E, F, d, e, f)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Sequence of entity 3 (H, h), FASTA

>5D80_3 V-type proton ATPase subunit H (chains H, h)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Sequence of entity 4 (J, L, N, j, l, n), FASTA

>5D80_4 V-type proton ATPase subunit G (chains J, L, N, j, l, n)
MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDK
ELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHIN
AL

Sequence of entity 5 (I, K, M, i, k, m), FASTA

>5D80_5 V-type proton ATPase subunit E (chains I, K, M, i, k, m)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 6 (G, g), FASTA

>5D80_6 V-type proton ATPase subunit D (chains G, g)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 7 (O, o), FASTA

>5D80_7 V-type proton ATPase subunit F (chains O, o)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Primary citation

Crystal structure of yeast V1-ATPase in the autoinhibited state. Oot, R.A., Kane, P.M., Berry, E.A. et al. EMBO J (2016) 35:1694-1706. DOI 10.15252/embj.201593447 · PubMed

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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