7TMM: H-transporting two-sector ATPase

Complete V1 Complex from Saccharomyces cerevisiae. Determined by electron microscopy at 3.5 Å resolution. Released 6 Apr 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Saccharomyces cerevisiae
Chains: 16
Atoms: 33,713
Mol. weight: 644.6 kDa
Ligands: ADP
Released: 6 Apr 2022

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

Secondary structure: helices and β-sheets

7TMM contains 248 α-helices and 263 β-strands across 16 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: 31 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	1
β-strand	35-38	4	1
α-helix	43	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	139-143	5	7
β-strand	151-152	2	8
β-strand	157-161	5	7
β-strand	170-173	4	7
α-helix	174-175	2
β-strand	180-185	6	8
α-helix	186-187	2
β-strand	189-191	3	7
β-strand	196-202	7	8
β-strand	205-210	6	8
β-strand	213-216	4	4
α-helix	220-222	3
β-strand	225-226	2	9
β-strand	232	1	10
α-helix	238-243	6
β-strand	247	1	10
β-strand	252-253	2	11
α-helix	262-272	11
β-strand	277	1	12
β-strand	278-285	8	5
α-helix	287-296	10
α-helix	297-299	3
β-strand	301-302	2	13
α-helix	304-306	3
β-strand	309-310	2	13
α-helix	311-313	3
β-strand	315-321	7	5
α-helix	328-345	18
β-strand	349-352	4	12
β-strand	353-354	2	5
α-helix	357-371	15
α-helix	373-374	2
β-strand	375	1	14
α-helix	377-379	3
β-strand	381	1	14
α-helix	384-392	9
β-strand	398-399	2	9
α-helix	405	1
β-strand	407-408	2	9
β-strand	409-412	4	12
β-strand	413-414	2	11
α-helix	419-421	3
α-helix	426-432	7
β-strand	437-438	2	11
β-strand	441	1	15
α-helix	443-447	5
β-strand	454	1	15
β-strand	460-461	2	11
α-helix	468-471	4
α-helix	478-502	25
α-helix	504-506	3
α-helix	509-521	13
α-helix	522-526	5
α-helix	540-562	23
α-helix	567-573	7
α-helix	575-582	8
α-helix	583-586	4
α-helix	589-591	3
α-helix	593-615	23

Chain B: 20 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
β-strand	26-28	3	16
β-strand	34-35	2	16
β-strand	38-40	3	16
β-strand	48	1	3
β-strand	52-56	5	16
β-strand	62-67	6	16
β-strand	76-79	4	16
β-strand	87	1	17
β-strand	92-95	4	16
β-strand	101-104	4	18
β-strand	112-113	2	19
β-strand	119	1	19
α-helix	124-126	3
β-strand	130-133	4	18
α-helix	138	1
β-strand	139	1	6
α-helix	140	1
β-strand	144-145	2	20
β-strand	150	1	21
β-strand	151	1	22
α-helix	156-159	4
β-strand	165	1	21
β-strand	169	1	19
β-strand	172-174	3	23
α-helix	180-190	11
β-strand	193	1	22
β-strand	209-215	7	19
α-helix	219-232	14
α-helix	234-237	4
β-strand	238-243	6	19
α-helix	251-270	20
β-strand	273-279	7	19
α-helix	281-295	15
β-strand	301	1	24
β-strand	304	1	24
α-helix	308-316	9
β-strand	321-322	2	20
β-strand	328-331	4	19
β-strand	334-336	3	23
α-helix	338-340	3
α-helix	345-353	9
β-strand	356-357	2	25
β-strand	358-359	2	23
β-strand	360	1	26
α-helix	362-367	6
β-strand	373	1	26
β-strand	379-380	2	25
α-helix	396-420	25
α-helix	422-424	3
α-helix	427-439	13
α-helix	440-444	5
α-helix	454-465	12
α-helix	478-484	7

Chain C: 28 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	16
β-strand	34-38	5	16
α-helix	43	1
β-strand	44	1	17
β-strand	47-51	5	16
β-strand	56-64	9	16
β-strand	67-72	6	16
β-strand	80	1	27
β-strand	84-91	8	16
β-strand	93-96	4	28
β-strand	104-105	2	29
β-strand	111	1	29
α-helix	112-119	8
β-strand	123	1	30
β-strand	138-143	6	31
β-strand	151-152	2	32
β-strand	157-161	5	31
β-strand	170-173	4	31
α-helix	174-175	2
β-strand	180-185	6	32
α-helix	186-187	2
β-strand	189-192	4	31
β-strand	198-201	4	32
β-strand	209	1	32
β-strand	213-216	4	28
α-helix	220-222	3
β-strand	223-226	4	33
β-strand	232	1	34
α-helix	238-242	5
β-strand	247	1	34
β-strand	252-254	3	29
α-helix	262-272	11
β-strand	277-281	5	29
β-strand	285	1	35
α-helix	287-296	10
β-strand	301-303	3	36
β-strand	308-310	3	36
α-helix	311-314	4
β-strand	315-318	4	29
β-strand	321	1	35
α-helix	326-345	20
β-strand	349-354	6	29
α-helix	357-371	15
α-helix	373-374	2
β-strand	375	1	37
α-helix	377-379	3
β-strand	381	1	37
α-helix	384-392	9
β-strand	398-400	3	33
α-helix	405	1
β-strand	407-408	2	33
β-strand	409-415	7	29
α-helix	419-421	3
α-helix	426-434	9
β-strand	437-438	2	29
β-strand	441	1	38
α-helix	443-447	5
β-strand	454	1	38
β-strand	460-461	2	29
α-helix	468-474	7
α-helix	478-501	24
α-helix	504-506	3
α-helix	509-524	16
α-helix	540-562	23
α-helix	567-573	7
α-helix	575-583	9
α-helix	584-586	3
α-helix	589-591	3
α-helix	593-613	21

Chain D: 26 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
β-strand	26-28	3	1
β-strand	31-33	3	1
β-strand	39-41	3	1
β-strand	48	1	27
β-strand	52-56	5	1
β-strand	62-67	6	1
β-strand	70-71	2	16
β-strand	74	1	16
β-strand	76-79	4	1
β-strand	87	1	39
β-strand	92-95	4	1
β-strand	101-104	4	40
α-helix	106-108	3
β-strand	112-113	2	41
β-strand	119	1	41
α-helix	124-126	3
β-strand	130-133	4	40
α-helix	138	1
β-strand	139	1	30
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	42
β-strand	150-152	3	43
α-helix	156-159	4
β-strand	164-165	2	43
β-strand	169	1	41
β-strand	172-174	3	44
α-helix	180-190	11
β-strand	192-193	2	43
β-strand	208-217	10	41
α-helix	219-232	14
α-helix	234-236	3
β-strand	240-244	5	41
α-helix	249-264	16
α-helix	265-269	5
β-strand	273-278	6	41
α-helix	281-292	12
α-helix	297-299	3
α-helix	308-316	9
β-strand	321-322	2	42
β-strand	328-331	4	41
β-strand	334-336	3	44
α-helix	338-340	3
α-helix	345-353	9
β-strand	356-357	2	45
β-strand	358-359	2	44
β-strand	360	1	46
α-helix	361	1
α-helix	362-367	6
β-strand	373	1	46
β-strand	379-380	2	45
α-helix	383-386	4
α-helix	396-420	25
α-helix	427-439	13
α-helix	440-444	5
α-helix	454-465	12
α-helix	470-472	3
α-helix	478-483	6

Chain E: 26 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
β-strand	44	1	39
β-strand	48-51	4	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	47
β-strand	84-87	4	1
β-strand	93-96	4	48
β-strand	104-105	2	49
β-strand	111	1	49
α-helix	112-119	8
β-strand	123	1	50
β-strand	139-143	5	51
β-strand	151-152	2	52
β-strand	157-161	5	51
β-strand	170-173	4	51
α-helix	174-175	2
β-strand	180-181	2	52
β-strand	182-185	4	53
α-helix	186-187	2
β-strand	189-191	3	51
β-strand	198-200	3	53
β-strand	207-209	3	53
β-strand	213-216	4	48
α-helix	220-222	3
β-strand	225-226	2	49
β-strand	232-233	2	54
α-helix	238-243	6
β-strand	246-247	2	54
β-strand	251	1	49
β-strand	254	1	55
α-helix	265-271	7
β-strand	277-282	6	49
β-strand	285	1	56
α-helix	287-296	10
β-strand	301-302	2	57
β-strand	309-310	2	57
β-strand	315-318	4	49
β-strand	321	1	56
α-helix	326-345	20
β-strand	349-355	7	49
α-helix	357-371	15
α-helix	373-375	3
β-strand	376	1	58
β-strand	380	1	58
α-helix	384-392	9
β-strand	396-399	4	49
α-helix	405	1
β-strand	407-414	8	49
β-strand	415	1	55
α-helix	426-431	6
β-strand	437-438	2	59
α-helix	440	1
β-strand	441	1	60
α-helix	442	1
α-helix	443-447	5
β-strand	454	1	60
β-strand	460-461	2	59
α-helix	468-474	7
α-helix	478-502	25
α-helix	509-520	12
α-helix	521-526	6
α-helix	540-562	23
α-helix	567-573	7
α-helix	575-583	9
α-helix	584-586	3
α-helix	589-591	3
α-helix	593-610	18

Chain F: 26 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	61
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	47
β-strand	53-56	4	61
β-strand	62-64	3	61
β-strand	65-70	6	1
β-strand	75-79	5	1
β-strand	87	1	2
β-strand	92-95	4	61
β-strand	101-104	4	62
α-helix	106-108	3
β-strand	112-113	2	63
β-strand	119	1	63
β-strand	130-133	4	62
α-helix	138	1
β-strand	139	1	50
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	64
α-helix	146	1
β-strand	150-152	3	65
α-helix	156-159	4
α-helix	163	1
β-strand	164-165	2	65
β-strand	172-174	3	66
α-helix	180-189	10
β-strand	192-193	2	65
β-strand	209-215	7	63
α-helix	219-231	13
α-helix	234-237	4
β-strand	238-243	6	63
α-helix	251-253	3
α-helix	255-269	15
β-strand	273-277	5	63
α-helix	281-294	14
α-helix	297-298	2
β-strand	299	1	67
α-helix	301-303	3
β-strand	305	1	67
α-helix	308-316	9
β-strand	321-322	2	64
β-strand	328-331	4	63
β-strand	334-336	3	66
α-helix	338-340	3
α-helix	345-353	9
β-strand	357	1	68
β-strand	358-359	2	66
β-strand	360	1	69
α-helix	362-367	6
β-strand	373	1	69
β-strand	379	1	68
α-helix	383-386	4
α-helix	396-420	25
α-helix	427-439	13
α-helix	440-444	5
α-helix	454-465	12
α-helix	470-472	3
α-helix	478-484	7

Chain G: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	13-48	36
α-helix	51-112	62
α-helix	114-132	19
β-strand	136-140	5	61
α-helix	146-163	18
α-helix	167-169	3
β-strand	171-174	4	61
β-strand	187-191	5	61
β-strand	197-202	6	61
α-helix	203-222	20
α-helix	224-226	3

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-102	97

8 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-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 C	O	protein	392	Saccharomyces cerevisiae	P31412
V-type proton ATPase subunit H	P	protein	478	Saccharomyces cerevisiae	P41807

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

>7TMM_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

>7TMM_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

>7TMM_3 V-ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

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

>7TMM_4 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 5 (M), FASTA

>7TMM_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 6 (N), FASTA

>7TMM_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 7 (O), FASTA

>7TMM_7 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 8 (P), FASTA

>7TMM_8 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

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…
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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