7TMP: H-transporting two-sector ATPase

V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2. 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: 32,105
Mol. weight: 600.38 kDa
Ligands: MG, ADP
Released: 6 Apr 2022

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

Secondary structure: helices and β-sheets

7TMP contains 214 α-helices and 229 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: 29 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	29-31	3	1
β-strand	34-37	4	1
α-helix	43-44	2
β-strand	47-51	5	1
β-strand	56-60	5	1
β-strand	63	1	2
β-strand	68-72	5	1
β-strand	85-91	7	1
β-strand	93-96	4	3
α-helix	100-102	3
β-strand	104-105	2	4
α-helix	112-119	8
β-strand	123	1	5
α-helix	124-125	2
β-strand	139-143	5	6
β-strand	151-152	2	7
β-strand	157-161	5	6
β-strand	170-173	4	6
α-helix	174-175	2
β-strand	180-185	6	7
β-strand	189-191	3	6
β-strand	198-202	5	7
β-strand	205-209	5	7
β-strand	213-216	4	3
α-helix	220-222	3
β-strand	225-226	2	8
β-strand	232	1	9
α-helix	238-242	5
β-strand	247	1	9
β-strand	251-253	3	4
α-helix	262-272	11
β-strand	277-285	9	4
α-helix	287-299	13
β-strand	301-302	2	10
α-helix	304-306	3
β-strand	309-310	2	10
α-helix	311-314	4
β-strand	315-321	7	4
α-helix	328-345	18
β-strand	349-354	6	4
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	8
α-helix	405	1
β-strand	407-408	2	8
β-strand	409-414	6	4
α-helix	419-421	3
α-helix	426-434	9
β-strand	437-438	2	4
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	4
α-helix	464-473	10
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	575-582	8
α-helix	583-586	4
α-helix	589-591	3
α-helix	593-615	23

Chain B: 22 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	15-19	5
β-strand	26-28	3	13
β-strand	31-35	5	13
β-strand	38-42	5	13
β-strand	52-56	5	13
α-helix	57	1
β-strand	62-67	6	13
β-strand	69-70	2	1
β-strand	74-79	6	13
β-strand	87	1	14
β-strand	92-95	4	13
β-strand	101-104	4	15
α-helix	106-108	3
β-strand	112-113	2	16
β-strand	119	1	16
α-helix	124-126	3
β-strand	130-133	4	15
α-helix	138	1
β-strand	139	1	5
α-helix	140	1
β-strand	144-145	2	17
β-strand	150-151	2	18
α-helix	156	1
α-helix	157-161	5
β-strand	164-165	2	18
β-strand	172-173	2	16
α-helix	180-190	11
β-strand	193	1	18
β-strand	211-217	7	16
α-helix	219-232	14
α-helix	234-237	4
β-strand	239-244	6	16
α-helix	254-268	15
β-strand	273-279	7	16
α-helix	281-294	14
α-helix	308-316	9
β-strand	321-322	2	17
β-strand	325	1	17
β-strand	328-331	4	16
β-strand	334	1	16
α-helix	345-353	9
β-strand	356-357	2	19
β-strand	358-359	2	16
β-strand	360	1	20
α-helix	362-367	6
β-strand	373	1	20
β-strand	379-380	2	19
α-helix	381-383	3
α-helix	396-420	25
α-helix	427-439	13
α-helix	440-444	5
α-helix	454-466	13
α-helix	478-484	7

Chain C: 25 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	13
β-strand	34-38	5	13
α-helix	43	1
β-strand	44	1	14
β-strand	47-51	5	13
β-strand	56-64	9	13
β-strand	67-72	6	13
α-helix	79	1
β-strand	80	1	21
β-strand	84-91	8	13
β-strand	93-96	4	22
β-strand	104-105	2	23
α-helix	112-119	8
β-strand	123	1	24
β-strand	138-143	6	25
β-strand	151-152	2	26
β-strand	157-162	6	25
β-strand	170-173	4	25
β-strand	180-185	6	26
β-strand	189-192	4	25
β-strand	198-201	4	26
β-strand	207-209	3	26
β-strand	213-216	4	22
α-helix	220-222	3
β-strand	223-225	3	27
β-strand	232	1	28
α-helix	238-242	5
β-strand	247	1	28
β-strand	251-254	4	23
α-helix	262-271	10
β-strand	277-281	5	23
α-helix	287-296	10
α-helix	297-299	3
β-strand	302	1	29
β-strand	309	1	29
α-helix	311-314	4
β-strand	315-318	4	23
α-helix	326-345	20
β-strand	349-354	6	23
α-helix	357-371	15
α-helix	373-374	2
β-strand	375-377	3	30
β-strand	380-381	2	30
α-helix	384-393	10
β-strand	398-400	3	27
α-helix	405	1
β-strand	407-408	2	27
β-strand	409-415	7	23
α-helix	419-421	3
α-helix	426-434	9
β-strand	437-438	2	23
β-strand	441	1	31
α-helix	443-447	5
β-strand	454	1	31
β-strand	460-461	2	23
α-helix	464-474	11
α-helix	478-501	24
α-helix	509-520	12
α-helix	521-526	6
α-helix	540-563	24
α-helix	567-573	7
α-helix	575-583	9
α-helix	594-614	21

Chain D: 23 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
β-strand	27-28	2	13
β-strand	31-35	5	13
β-strand	38-41	4	13
α-helix	47	1
β-strand	48	1	21
β-strand	52-56	5	13
β-strand	62-71	10	13
β-strand	74-79	6	13
β-strand	87	1	32
β-strand	92-95	4	13
β-strand	101-104	4	33
α-helix	106-108	3
β-strand	112-113	2	34
β-strand	119	1	34
α-helix	124-126	3
β-strand	130-133	4	33
α-helix	138	1
β-strand	139	1	24
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	35
β-strand	150	1	36
β-strand	151-152	2	37
α-helix	156-161	6
β-strand	165	1	36
β-strand	169	1	34
β-strand	172-174	3	38
α-helix	180-190	11
β-strand	192-193	2	37
β-strand	208	1	39
β-strand	211-217	7	34
α-helix	219-232	14
α-helix	234-237	4
β-strand	239-244	6	34
α-helix	249-270	22
β-strand	273	1	39
β-strand	276-279	4	34
α-helix	281-294	14
α-helix	297-299	3
α-helix	308-317	10
β-strand	321-322	2	35
β-strand	331	1	34
β-strand	335-336	2	38
α-helix	345-353	9
β-strand	356-360	5	38
α-helix	362-365	4
β-strand	373-380	8	38
α-helix	383-386	4
α-helix	396-420	25
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	478-484	7

Chain E: 25 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	13
β-strand	34-38	5	13
β-strand	44	1	32
β-strand	48-51	4	13
β-strand	56-64	9	13
β-strand	67-72	6	13
β-strand	80	1	40
β-strand	84-87	4	13
β-strand	93-96	4	41
β-strand	104-105	2	42
β-strand	111	1	42
α-helix	112-119	8
β-strand	123	1	43
β-strand	139-143	5	44
β-strand	151-152	2	45
β-strand	157	1	46
β-strand	159-161	3	44
α-helix	171-172	2
β-strand	173	1	46
α-helix	174-175	2
β-strand	180-181	2	45
β-strand	182-185	4	47
α-helix	186-187	2
β-strand	189-191	3	44
β-strand	196-200	5	47
β-strand	207-210	4	47
β-strand	213-216	4	41
α-helix	220-222	3
β-strand	225	1	48
α-helix	227-229	3
β-strand	232-233	2	49
α-helix	238-242	5
β-strand	246-247	2	49
β-strand	254-255	2	50
α-helix	260-272	13
β-strand	277-285	9	42
α-helix	287-296	10
β-strand	301-302	2	51
β-strand	309-310	2	51
α-helix	311-313	3
β-strand	315	1	42
β-strand	317-321	5	42
α-helix	326-345	20
β-strand	349-355	7	42
α-helix	357-371	15
α-helix	373-374	2
β-strand	375-377	3	52
β-strand	380-381	2	52
α-helix	384-392	9
β-strand	398-400	3	48
α-helix	405	1
β-strand	406-408	3	48
β-strand	409-414	6	42
β-strand	415-416	2	50
α-helix	426-434	9
β-strand	437-438	2	53
β-strand	441	1	54
α-helix	443-447	5
β-strand	454	1	54
β-strand	460-461	2	53
α-helix	464-474	11
α-helix	478-502	25
α-helix	509-520	12
α-helix	521-525	5
α-helix	540-563	24
α-helix	567-573	7
α-helix	575-583	9
α-helix	593-610	18

Chain F: 21 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
β-strand	26-28	3	13
β-strand	32-35	4	13
β-strand	38-41	4	13
β-strand	48	1	40
β-strand	52-56	5	13
β-strand	62-70	9	13
β-strand	75-79	5	13
β-strand	92-95	4	13
β-strand	101-104	4	55
β-strand	111-113	3	56
β-strand	119	1	56
α-helix	124-126	3
β-strand	130-133	4	55
β-strand	139	1	43
α-helix	141-143	3
β-strand	144-145	2	57
β-strand	150-151	2	58
α-helix	156-159	4
β-strand	164-165	2	58
β-strand	172-175	4	59
α-helix	180-189	10
β-strand	193	1	58
β-strand	209-215	7	56
α-helix	219-232	14
β-strand	238-243	6	56
α-helix	251-264	14
α-helix	265-269	5
β-strand	274-276	3	56
β-strand	279	1	56
α-helix	281-294	14
α-helix	308-316	9
β-strand	321-322	2	57
β-strand	328	1	57
β-strand	329	1	56
β-strand	334-337	4	59
α-helix	345-353	9
β-strand	357-360	4	59
α-helix	361	1
α-helix	362-367	6
β-strand	373-379	7	59
α-helix	383-386	4
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	470-472	3
α-helix	478-484	7

Chain G: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	46-112	67
α-helix	114-132	19
β-strand	136-141	6	13
α-helix	146-163	18
α-helix	167-169	3
β-strand	171-174	4	13
α-helix	178-180	3
β-strand	188-191	4	13
β-strand	197-200	4	13
α-helix	203-213	11
α-helix	215-222	8
α-helix	224-226	3

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-103	74

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-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

>7TMP_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

>7TMP_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

>7TMP_3 V-ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

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

>7TMP_4 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 5 (M), FASTA

>7TMP_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 6 (N), FASTA

>7TMP_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 7 (P), FASTA

>7TMP_7 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
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
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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