7TMO: H-transporting two-sector ATPase

V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1. Determined by electron microscopy at 3.3 Å resolution. Released 6 Apr 2022.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae
Chains: 15
Atoms: 31,559
Mol. weight: 600.91 kDa
Ligands: ADP, MG, ATP
Released: 6 Apr 2022

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

Secondary structure: helices and β-sheets

7TMO contains 213 α-helices and 238 β-strands across 15 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: 28 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
α-helix	43-44	2
β-strand	47-51	5	1
β-strand	56-62	7	1
β-strand	68-72	5	1
α-helix	79-80	2
β-strand	84-91	8	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	180-185	6	6
α-helix	186-187	2
β-strand	189-191	3	5
β-strand	198-202	5	6
β-strand	205-209	5	6
β-strand	213-216	4	2
α-helix	220-222	3
β-strand	225-226	2	7
β-strand	232	1	8
α-helix	238-242	5
β-strand	247	1	8
β-strand	252-253	2	9
α-helix	262-272	11
β-strand	277-283	7	3
α-helix	287-296	10
β-strand	301-302	2	10
α-helix	304-306	3
β-strand	309-310	2	10
α-helix	311-314	4
β-strand	315-320	6	3
α-helix	328-345	18
β-strand	349-354	6	3
α-helix	357-371	15
β-strand	377	1	11
β-strand	380	1	11
α-helix	384-393	10
β-strand	398-399	2	7
α-helix	405	1
β-strand	407-408	2	7
β-strand	409-410	2	3
β-strand	413-414	2	9
α-helix	426-434	9
β-strand	437-438	2	9
β-strand	441	1	12
α-helix	443-446	4
α-helix	447-449	3
β-strand	454	1	12
β-strand	460-461	2	9
α-helix	468-474	7
α-helix	478-502	25
α-helix	509-520	12
α-helix	521-526	6
α-helix	540-563	24
α-helix	567-573	7
α-helix	575-582	8
α-helix	583-586	4
α-helix	589-591	3
α-helix	593-614	22

Chain B: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
β-strand	33-35	3	1
β-strand	38-42	5	1
β-strand	51-56	6	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	92-99	8	1
β-strand	101-104	4	13
α-helix	106-108	3
β-strand	112-113	2	14
β-strand	119	1	14
α-helix	124-126	3
β-strand	130-133	4	13
α-helix	138	1
β-strand	139	1	4
α-helix	140	1
β-strand	144-145	2	14
α-helix	146-147	2
β-strand	150-151	2	15
α-helix	156	1
α-helix	157-161	5
β-strand	164-165	2	15
β-strand	172-173	2	14
α-helix	180-190	11
β-strand	193	1	15
β-strand	209-217	9	14
α-helix	219-232	14
α-helix	234-237	4
β-strand	240-244	5	14
α-helix	254-268	15
β-strand	273-279	7	14
α-helix	281-294	14
α-helix	308-316	9
β-strand	320-322	3	14
β-strand	325-331	7	14
β-strand	334	1	14
α-helix	345-353	9
β-strand	356-360	5	14
α-helix	361	1
α-helix	362-367	6
β-strand	373-380	8	14
α-helix	396-420	25
α-helix	427-439	13
α-helix	440-444	5
α-helix	454-467	14
α-helix	478-484	7

Chain C: 25 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	1
β-strand	31	1	16
β-strand	35-38	4	1
α-helix	43-44	2
β-strand	47-51	5	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	85-91	7	1
β-strand	93-96	4	17
β-strand	104-105	2	18
β-strand	111	1	18
α-helix	112-119	8
β-strand	123	1	19
β-strand	138-143	6	20
β-strand	151-152	2	21
β-strand	157-161	5	20
β-strand	170-173	4	20
β-strand	180-185	6	21
β-strand	189-192	4	20
β-strand	198-201	4	21
β-strand	208-209	2	21
β-strand	213-216	4	17
α-helix	220-222	3
β-strand	223-226	4	22
β-strand	232-233	2	23
α-helix	238-242	5
β-strand	246-247	2	23
β-strand	251-254	4	18
α-helix	265-271	7
β-strand	277-280	4	18
α-helix	287-299	13
β-strand	301	1	24
β-strand	310	1	24
α-helix	311-313	3
β-strand	315-318	4	18
α-helix	326-344	19
β-strand	349-354	6	18
α-helix	357-371	15
α-helix	373-374	2
β-strand	375-377	3	25
β-strand	380-381	2	25
α-helix	384-394	11
β-strand	398-400	3	22
α-helix	405	1
β-strand	407-408	2	22
β-strand	409-415	7	18
α-helix	419-421	3
α-helix	426-434	9
β-strand	437-438	2	18
β-strand	441	1	26
α-helix	443-447	5
β-strand	454	1	26
β-strand	460-461	2	18
α-helix	464-474	11
α-helix	478-501	24
α-helix	504-506	3
α-helix	509-520	12
α-helix	521-526	6
α-helix	533-535	3
α-helix	540-563	24
α-helix	567-573	7
α-helix	575-586	12
α-helix	593-614	22

Chain D: 19 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	16
β-strand	31-35	5	16
β-strand	39-41	3	16
β-strand	51-56	6	16
β-strand	62-71	10	16
β-strand	74-79	6	16
β-strand	87	1	27
β-strand	92-99	8	16
β-strand	101-104	4	28
β-strand	112-113	2	29
β-strand	119	1	29
β-strand	130-133	4	28
α-helix	138	1
β-strand	139	1	19
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	30
β-strand	150	1	31
β-strand	151-152	2	32
α-helix	156-161	6
β-strand	165	1	31
β-strand	169	1	33
β-strand	172-173	2	29
α-helix	180-190	11
β-strand	192-193	2	32
β-strand	208	1	34
β-strand	210	1	35
β-strand	212-217	6	29
α-helix	219-231	13
α-helix	234-237	4
β-strand	238	1	35
β-strand	240-244	5	29
α-helix	249-270	22
β-strand	273	1	34
β-strand	276	1	33
β-strand	277-279	3	29
α-helix	281-293	13
α-helix	308-317	10
β-strand	321-322	2	30
β-strand	328	1	34
β-strand	331	1	33
β-strand	334	1	29
α-helix	338-340	3
α-helix	345-353	9
β-strand	357-360	4	29
α-helix	362-367	6
β-strand	373-379	7	29
α-helix	383-386	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

Chain E: 26 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	16
β-strand	34-38	5	16
β-strand	44	1	27
β-strand	47-51	5	36
β-strand	56-57	2	36
β-strand	60-64	5	16
β-strand	68-71	4	16
β-strand	80	1	37
β-strand	84-85	2	16
β-strand	86-91	6	36
β-strand	93-96	4	38
β-strand	104-105	2	39
β-strand	111	1	39
α-helix	112-119	8
β-strand	123	1	40
α-helix	138	1
β-strand	139-141	3	41
β-strand	151-152	2	42
β-strand	157-161	5	43
β-strand	170-173	4	43
α-helix	174-175	2
β-strand	180-181	2	42
β-strand	182-185	4	44
α-helix	186-187	2
β-strand	189-191	3	41
β-strand	198-200	3	44
β-strand	207-209	3	44
β-strand	213-216	4	38
α-helix	220-222	3
β-strand	225-226	2	45
β-strand	232-233	2	46
α-helix	238-243	6
β-strand	246-247	2	46
β-strand	251-253	3	47
α-helix	262-271	10
β-strand	277	1	47
β-strand	278-281	4	39
β-strand	285	1	48
α-helix	287-296	10
β-strand	301-302	2	49
β-strand	309-310	2	49
α-helix	311-313	3
β-strand	315-318	4	39
β-strand	321	1	48
α-helix	326-345	20
β-strand	349-352	4	47
β-strand	353-354	2	39
α-helix	357-371	15
α-helix	373-375	3
β-strand	377	1	50
β-strand	380	1	50
α-helix	384-392	9
β-strand	398-399	2	45
α-helix	400	1
α-helix	405	1
β-strand	407-408	2	45
β-strand	409-414	6	47
α-helix	419-421	3
α-helix	426-434	9
β-strand	437-438	2	47
β-strand	441	1	51
α-helix	443-447	5
β-strand	454	1	51
β-strand	460-461	2	47
α-helix	464-473	10
α-helix	478-502	25
α-helix	509-524	16
α-helix	540-563	24
α-helix	567-573	7
α-helix	575-583	9
α-helix	589-591	3
α-helix	592-612	21

Chain F: 25 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	52
β-strand	31	1	52
β-strand	38-41	4	52
β-strand	48	1	37
β-strand	52-56	5	52
β-strand	62-70	9	52
β-strand	75-79	5	52
β-strand	92-95	4	52
β-strand	101-104	4	53
α-helix	106-108	3
β-strand	112-113	2	54
β-strand	119	1	54
α-helix	124-126	3
β-strand	130-133	4	53
α-helix	138	1
β-strand	139	1	40
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	55
β-strand	150-153	4	56
α-helix	156-159	4
β-strand	164-165	2	56
β-strand	169	1	57
β-strand	172-174	3	54
α-helix	180-189	10
β-strand	191-193	3	56
β-strand	209-217	9	54
α-helix	219-232	14
α-helix	234-236	3
β-strand	238-244	7	54
α-helix	251-264	14
α-helix	265-270	6
β-strand	273-279	7	54
α-helix	281-294	14
α-helix	297-298	2
β-strand	299	1	58
α-helix	301-303	3
β-strand	305	1	58
α-helix	308-316	9
β-strand	321-322	2	55
β-strand	328-329	2	54
β-strand	331	1	57
β-strand	334-336	3	54
α-helix	345-353	9
β-strand	356-357	2	59
β-strand	358-359	2	54
β-strand	360	1	60
α-helix	361	1
α-helix	362-367	6
β-strand	373	1	60
β-strand	379-380	2	59
α-helix	383-386	4
β-strand	389	1	61
β-strand	392	1	61
α-helix	396-419	24
α-helix	422-424	3
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	478-484	7

Chain G: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	33-113	81
α-helix	117-132	16
β-strand	136-141	6	1
α-helix	143-163	21
α-helix	167-169	3
β-strand	171-174	4	1
β-strand	188-192	5	1
β-strand	197-200	4	1
α-helix	203-213	11
α-helix	215-223	9

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	33-60	28
α-helix	64-102	39

7 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
H(+)-transporting two-sector ATPase	A, C, E	protein	639	Saccharomyces cerevisiae	P17255 (AlphaFold model)
Vacuolar proton pump subunit B	B, D, F	protein	517	Saccharomyces cerevisiae	P16140 (AlphaFold model)
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae	P22203 (AlphaFold model)
V-type proton ATPase subunit G	H, J, L	protein	114	Saccharomyces cerevisiae	P48836 (AlphaFold model)
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae	P32610
V-type proton ATPase subunit F	N	protein	118	Saccharomyces cerevisiae	P39111
V-type proton ATPase subunit H	P	protein	478	Saccharomyces cerevisiae	P41807

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

>7TMO_1 H(+)-transporting two-sector ATPase (chains A, C, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTDDYKDHDGDYKDHDIDYKDDDDK

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

>7TMO_2 Vacuolar proton pump subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

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

>7TMO_3 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

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

>7TMO_4 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 5 (M), FASTA

>7TMO_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 6 (N), FASTA

>7TMO_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 7 (P), FASTA

>7TMO_7 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Coordinated conformational changes in the V 1 complex during V-ATPase reversible dissociation. Vasanthakumar, T., Keon, K.A., Bueler, S.A. et al. Nat Struct Mol Biol (2022) 29:430-439. DOI 10.1038/s41594-022-00757-z · 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…
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…
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae

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