5BW9: Yeast V1-ATPase in the Autoinhibited Form

Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form. Determined by X-ray diffraction at 7.0 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 7.0 Å
Organism: Saccharomyces cerevisiae
Chains: 28
Atoms: 44,760
Mol. weight: 1162.57 kDa
Released: 8 Jun 2016

Explore 5BW9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5BW9 contains 387 α-helices and 399 β-strands across 28 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.

Chains a and A: 25 helices, 32 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	68-73	6	53
β-strand	81	1	54
β-strand	85-88	4	53
β-strand	94-97	4	55
β-strand	105-106	2	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	170	1
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	224-227	4	56
β-strand	233	1	60
α-helix	234-235	2
α-helix	239-243	5
β-strand	248	1	60
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	61
β-strand	311	1	61
β-strand	316-319	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	397-401	5	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	591-593	3
α-helix	595-611	17

Chain b: 24 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	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	62
β-strand	85-92	8	53
β-strand	94-97	4	63
β-strand	105-106	2	64
β-strand	112	1	64
α-helix	113-120	8
β-strand	124	1	65
β-strand	140-143	4	66
α-helix	147-148	2
β-strand	152-154	3	67
β-strand	158-162	5	66
β-strand	171-174	4	66
α-helix	175-176	2
β-strand	180-185	6	67
α-helix	187-188	2
β-strand	190-192	3	66
β-strand	197-203	7	67
β-strand	206-211	6	67
β-strand	214-217	4	63
α-helix	221-223	3
β-strand	226-227	2	64
β-strand	233	1	68
α-helix	234-235	2
α-helix	239-243	5
β-strand	248	1	68
β-strand	252-256	5	64
α-helix	263-273	11
β-strand	280-286	7	64
α-helix	288-297	10
β-strand	302	1	69
β-strand	311	1	69
β-strand	317-322	6	64
α-helix	328-345	18
β-strand	350-356	7	64
α-helix	358-371	14
α-helix	374-376	3
β-strand	378	1	70
β-strand	381	1	70
α-helix	385-395	11
β-strand	397-400	4	64
β-strand	408-417	10	64
α-helix	420-422	3
α-helix	427-435	9
β-strand	438-439	2	64
β-strand	462	1	64
α-helix	465-472	8
α-helix	473-475	3
α-helix	479-502	24
α-helix	510-522	13
α-helix	523-527	5
α-helix	541-562	22
α-helix	568-573	6
α-helix	576-583	8
α-helix	595-612	18

Chain B: 24 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	25-32	8	1
β-strand	35-39	5	1
β-strand	48-52	5	1
β-strand	57-65	9	1
β-strand	68-73	6	1
β-strand	81	1	11
β-strand	85-92	8	1
β-strand	94-97	4	12
β-strand	105-106	2	13
β-strand	112	1	13
α-helix	113-120	8
β-strand	124	1	14
β-strand	140-143	4	15
α-helix	147-148	2
β-strand	152-154	3	16
β-strand	158-162	5	15
β-strand	171-174	4	15
α-helix	175-176	2
β-strand	180-185	6	16
α-helix	187-188	2
β-strand	190-192	3	15
β-strand	197-203	7	16
β-strand	206-211	6	16
β-strand	214-217	4	12
α-helix	221-223	3
β-strand	226-227	2	13
β-strand	233	1	17
α-helix	234-235	2
α-helix	239-243	5
β-strand	248	1	17
β-strand	252-256	5	13
α-helix	263-273	11
β-strand	280-286	7	13
α-helix	288-297	10
β-strand	302	1	18
β-strand	311	1	18
β-strand	317-322	6	13
α-helix	328-345	18
β-strand	350-356	7	13
α-helix	358-371	14
α-helix	374-376	3
β-strand	378	1	19
β-strand	381	1	19
α-helix	385-395	11
β-strand	397-400	4	13
β-strand	408-417	10	13
α-helix	420-422	3
α-helix	427-435	9
β-strand	438-439	2	13
β-strand	462	1	13
α-helix	465-472	8
α-helix	473-475	3
α-helix	479-502	24
α-helix	510-522	13
α-helix	523-527	5
α-helix	541-562	22
α-helix	568-573	6
α-helix	576-583	8
α-helix	595-612	18

Chain c: 21 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-32	8	53
β-strand	35-39	5	53
β-strand	49-52	4	53
β-strand	57-65	9	53
β-strand	68-73	6	53
β-strand	81	1	71
β-strand	85-87	3	53
β-strand	95-97	3	72
β-strand	105-107	3	73
β-strand	112	1	73
α-helix	113-120	8
β-strand	124	1	74
β-strand	140-142	3	75
β-strand	152-153	2	76
β-strand	158-161	4	77
β-strand	162	1	75
β-strand	172-174	3	77
α-helix	175-176	2
β-strand	181-186	6	76
β-strand	190-192	3	75
β-strand	197-203	7	76
β-strand	206-211	6	76
β-strand	214-216	3	72
α-helix	221-223	3
β-strand	226-227	2	73
β-strand	233	1	78
α-helix	239-243	5
β-strand	248	1	78
β-strand	252-254	3	73
α-helix	263-272	10
β-strand	278-286	9	73
α-helix	288-300	13
β-strand	316-322	7	73
α-helix	328-346	19
β-strand	350-355	6	73
α-helix	358-371	14
α-helix	378-380	3
α-helix	385-393	9
β-strand	397-400	4	73
β-strand	408-415	8	73
α-helix	420-422	3
α-helix	427-433	7
β-strand	438-439	2	73
α-helix	444-447	4
β-strand	461-462	2	73
α-helix	465-475	11
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 C: 21 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-32	8	1
β-strand	35-39	5	1
β-strand	49-52	4	1
β-strand	57-65	9	1
β-strand	68-73	6	1
β-strand	81	1	20
β-strand	85-87	3	1
β-strand	95-97	3	21
β-strand	105-107	3	22
β-strand	112	1	22
α-helix	113-120	8
β-strand	124	1	23
β-strand	140-142	3	24
β-strand	152-153	2	25
β-strand	158-161	4	26
β-strand	162	1	24
β-strand	172-174	3	26
α-helix	175-176	2
β-strand	181-186	6	25
β-strand	190-192	3	24
β-strand	197-203	7	25
β-strand	206-211	6	25
β-strand	214-216	3	21
α-helix	221-223	3
β-strand	224-227	4	22
β-strand	233	1	27
α-helix	239-243	5
β-strand	248	1	27
β-strand	252-254	3	22
α-helix	263-272	10
β-strand	278-286	9	22
α-helix	288-300	13
β-strand	316-322	7	22
α-helix	328-346	19
β-strand	350-355	6	22
α-helix	358-371	14
α-helix	378-380	3
α-helix	385-393	9
β-strand	397-401	5	22
β-strand	408-415	8	22
α-helix	420-422	3
α-helix	427-433	7
β-strand	438-439	2	22
α-helix	444-447	4
β-strand	461-462	2	22
α-helix	465-475	11
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

Chains d and 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	51-56	6	53
β-strand	62-71	10	53
β-strand	75-79	5	53
β-strand	92-99	8	53
β-strand	101-104	4	79
β-strand	112-113	2	80
β-strand	119	1	80
α-helix	125-128	4
β-strand	130-133	4	79
α-helix	138	1
β-strand	139	1	57
α-helix	140	1
β-strand	144-145	2	81
β-strand	150-151	2	82
β-strand	164-165	2	82
β-strand	169	1	80
β-strand	172-174	3	83
α-helix	180-192	13
α-helix	207-208	2
β-strand	209-217	9	80
α-helix	219-232	14
β-strand	238-244	7	80
α-helix	249-264	16
α-helix	265-269	5
β-strand	274-278	5	80
α-helix	281-293	13
α-helix	297-299	3
α-helix	308-313	6
α-helix	316-318	3
β-strand	320	1	80
β-strand	321-322	2	81
β-strand	329-333	5	80
β-strand	334-336	3	83
α-helix	337	1
α-helix	338-340	3
α-helix	345-353	9
β-strand	358	1	83
α-helix	362-365	4
α-helix	382-384	3
α-helix	396-417	22
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, 32 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	53
β-strand	31	1	53
β-strand	33-34	2	53
β-strand	39-41	3	53
α-helix	47	1
β-strand	48	1	62
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	84
β-strand	112-114	3	85
β-strand	119	1	85
α-helix	125-128	4
β-strand	130-132	3	84
α-helix	138	1
β-strand	139	1	65
α-helix	140	1
β-strand	144-145	2	85
β-strand	148	1	86
α-helix	157-161	5
β-strand	166	1	86
β-strand	169	1	85
β-strand	172-175	4	87
α-helix	180-194	15
α-helix	195-197	3
β-strand	209-217	9	85
α-helix	219-232	14
α-helix	234-236	3
β-strand	239-244	6	85
α-helix	249-268	20
β-strand	274-279	6	85
α-helix	281-294	14
β-strand	299	1	88
α-helix	301-303	3
β-strand	305	1	88
α-helix	308-316	9
β-strand	320-322	3	85
β-strand	328-333	6	85
β-strand	335-337	3	87
α-helix	338-340	3
α-helix	345-353	9
β-strand	356-357	2	89
β-strand	358-359	2	87
β-strand	360	1	90
β-strand	373	1	90
β-strand	379-380	2	89
α-helix	396-419	24
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	478-484	7

Chain f: 21 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	53
β-strand	33-35	3	53
β-strand	38-41	4	53
β-strand	48	1	71
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	91
α-helix	106-108	3
β-strand	112-114	3	92
β-strand	119	1	92
α-helix	125-128	4
β-strand	132-133	2	91
α-helix	138	1
β-strand	139	1	74
α-helix	140	1
β-strand	144-145	2	92
β-strand	172-174	3	93
α-helix	180-189	10
β-strand	208-214	7	92
β-strand	217	1	94
α-helix	219-232	14
α-helix	235-237	3
β-strand	239-242	4	92
β-strand	244	1	94
α-helix	254-265	12
α-helix	266-270	5
β-strand	273-279	7	92
α-helix	281-294	14
α-helix	301-303	3
α-helix	308-316	9
β-strand	320-322	3	92
β-strand	328-331	4	92
β-strand	334-336	3	93
α-helix	338-340	3
α-helix	345-353	9
β-strand	357	1	95
β-strand	358-359	2	93
β-strand	360	1	96
α-helix	362-367	6
β-strand	373	1	96
β-strand	379	1	95
α-helix	381-383	3
α-helix	396-419	24
α-helix	428-438	11
α-helix	439-443	5
α-helix	454-464	11
α-helix	478-481	4

17 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 D	G, g	protein	256	Saccharomyces cerevisiae	P32610 (AlphaFold model)
V-type proton ATPase subunit G	J, L, N, j, l, n	protein	122	Saccharomyces cerevisiae	P48836
V-type proton ATPase subunit E	I, K, M, i, k, m	protein	233	Saccharomyces cerevisiae	P22203

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

>5BW9_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

>5BW9_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

>5BW9_3 V-type proton ATPase subunit H (chains H, h)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Sequence of entity 4 (G, g), FASTA

>5BW9_4 V-type proton ATPase subunit D (chains G, g)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 5 (J, L, N, j, l, n), FASTA

>5BW9_5 V-type proton ATPase subunit G (chains J, L, N, j, l, n)
MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDK
ELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHIN
AL

Sequence of entity 6 (I, K, M, i, k, m), FASTA

>5BW9_6 V-type proton ATPase subunit E (chains I, K, M, i, k, m)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

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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