7FDE: Reconstituted V-ATPase, Oxr1 bound V1

CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1. Determined by electron microscopy at 3.8 Å resolution. Released 29 Dec 2021.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 16
Atoms: 39,557
Mol. weight: 615.34 kDa
Released: 29 Dec 2021

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

Secondary structure: helices and β-sheets

7FDE contains 202 α-helices and 273 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: 24 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	4
β-strand	29-31	3	5
β-strand	34-36	3	5
β-strand	48-51	4	5
β-strand	56-64	9	5
β-strand	67-72	6	5
β-strand	80	1	6
β-strand	84-85	2	4
β-strand	93-96	4	7
β-strand	104-105	2	8
β-strand	111	1	8
α-helix	112-119	8
β-strand	123	1	9
β-strand	139-143	5	10
β-strand	151-152	2	11
β-strand	159-161	3	10
β-strand	170-171	2	10
α-helix	174-175	2
β-strand	180-185	6	11
β-strand	189-191	3	10
β-strand	198-201	4	11
β-strand	209	1	11
β-strand	213-216	4	7
α-helix	220-222	3
β-strand	225-227	3	12
β-strand	232-233	2	13
α-helix	238-243	6
β-strand	246-247	2	13
β-strand	253	1	14
β-strand	255	1	15
α-helix	263-272	10
β-strand	277-281	5	8
β-strand	285	1	16
α-helix	288-296	9
α-helix	297-299	3
α-helix	312-314	3
β-strand	315-318	4	8
β-strand	321	1	16
α-helix	326-330	5
α-helix	332-345	14
β-strand	349	1	12
β-strand	350-353	4	8
α-helix	357-371	15
α-helix	377-379	3
α-helix	384-393	10
β-strand	396-399	4	12
β-strand	407-410	4	12
β-strand	413	1	8
β-strand	416	1	15
α-helix	426-434	9
β-strand	438	1	14
β-strand	441	1	17
α-helix	444-448	5
β-strand	454	1	17
β-strand	460	1	14
α-helix	464-474	11
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	575-584	10
α-helix	595-615	21

Chain B: 22 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	26-28	3	18
β-strand	31	1	18
β-strand	34	1	5
β-strand	38-41	4	18
β-strand	48	1	6
β-strand	53-56	4	18
β-strand	62	1	18
β-strand	65-67	3	18
β-strand	70	1	5
β-strand	75-79	5	18
β-strand	92-95	4	18
β-strand	101-104	4	19
α-helix	106-108	3
β-strand	112-113	2	20
β-strand	119	1	20
β-strand	130-133	4	19
α-helix	137-138	2
β-strand	139	1	9
α-helix	140	1
α-helix	141-143	3
β-strand	144	1	21
β-strand	150-151	2	22
β-strand	152	1	23
α-helix	156-162	7
β-strand	164-165	2	22
β-strand	169	1	20
β-strand	172	1	24
α-helix	180-190	11
β-strand	192	1	23
β-strand	208-213	6	20
β-strand	217	1	25
α-helix	219-231	13
α-helix	234-237	4
β-strand	240-241	2	20
β-strand	244	1	25
α-helix	249-270	22
β-strand	273-277	5	20
α-helix	282-290	9
α-helix	297-299	3
α-helix	301-303	3
α-helix	308-316	9
β-strand	322	1	21
β-strand	328	1	20
β-strand	331-332	2	20
β-strand	334	1	24
α-helix	345-353	9
β-strand	357	1	26
β-strand	358	1	24
α-helix	362-366	5
β-strand	379	1	26
α-helix	383-385	3
α-helix	396-419	24
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	478-484	7

Chain C: 22 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	5
β-strand	34-38	5	5
β-strand	48-51	4	5
β-strand	56-64	9	5
β-strand	67-72	6	5
β-strand	80	1	27
β-strand	84-86	3	5
β-strand	93-96	4	28
β-strand	105	1	29
β-strand	111	1	29
α-helix	112-119	8
β-strand	123	1	30
β-strand	139-143	5	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
β-strand	189-191	3	31
β-strand	198-201	4	32
β-strand	208	1	32
β-strand	213-216	4	28
α-helix	220-222	3
β-strand	225-226	2	33
β-strand	232-233	2	34
α-helix	238-243	6
β-strand	246-247	2	34
α-helix	262-272	11
β-strand	277	1	35
β-strand	278-285	8	29
α-helix	288-296	9
α-helix	297-299	3
β-strand	302-303	2	36
β-strand	307-308	2	36
α-helix	311-314	4
β-strand	315-321	7	29
α-helix	326-345	20
β-strand	349-350	2	35
β-strand	353	1	29
α-helix	357-371	15
β-strand	377	1	37
β-strand	380	1	37
α-helix	384-392	9
β-strand	398-399	2	33
β-strand	408	1	33
β-strand	409-410	2	35
β-strand	413	1	29
β-strand	419	1	38
β-strand	421	1	38
α-helix	426-434	9
β-strand	438	1	39
α-helix	443-447	5
β-strand	460	1	39
α-helix	464-474	11
α-helix	478-502	25
α-helix	509-520	12
α-helix	521-526	6
α-helix	533-535	3
α-helix	540-562	23
α-helix	567-583	17
α-helix	584-586	3
α-helix	595-615	21

Chain D: 24 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	17-19	3
β-strand	27-28	2	40
β-strand	31-35	5	5
β-strand	38-41	4	5
β-strand	48	1	27
β-strand	52-56	5	5
β-strand	62-70	9	5
β-strand	75-79	5	5
β-strand	87	1	41
β-strand	92	1	5
β-strand	93-94	2	40
β-strand	95	1	5
β-strand	101-104	4	42
α-helix	106-108	3
β-strand	111-113	3	43
β-strand	119	1	43
β-strand	130-133	4	42
α-helix	138	1
β-strand	139	1	30
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	44
β-strand	151-152	2	45
α-helix	156-159	4
β-strand	164	1	45
β-strand	169	1	43
β-strand	172	1	46
α-helix	180-190	11
β-strand	192-193	2	45
β-strand	209-214	6	43
β-strand	217	1	47
α-helix	219-232	14
α-helix	235-237	3
β-strand	238-241	4	43
β-strand	244	1	47
α-helix	251-253	3
α-helix	255-269	15
β-strand	274-279	6	43
α-helix	281-290	10
α-helix	301-303	3
α-helix	308-317	10
β-strand	320	1	48
β-strand	321-322	2	44
β-strand	329	1	48
β-strand	331	1	43
β-strand	334	1	46
α-helix	345-353	9
β-strand	358	1	46
β-strand	359-360	2	49
α-helix	362-366	5
β-strand	373-374	2	49
α-helix	383-386	4
α-helix	396-417	22
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	478-480	3
α-helix	481-485	5

Chain E: 24 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	5
β-strand	34-38	5	5
β-strand	44	1	41
β-strand	47	1	50
β-strand	48-51	4	5
β-strand	56-64	9	5
β-strand	67-72	6	5
β-strand	80	1	51
β-strand	84-85	2	5
β-strand	91	1	50
β-strand	93-95	3	52
β-strand	104-105	2	53
β-strand	111	1	53
α-helix	112-119	8
β-strand	123	1	54
β-strand	139-143	5	55
β-strand	151-152	2	56
β-strand	157	1	57
β-strand	159-161	3	55
β-strand	173	1	57
α-helix	174-175	2
β-strand	180-185	6	56
α-helix	186-187	2
β-strand	189-191	3	55
β-strand	198-201	4	56
β-strand	209	1	56
β-strand	214-216	3	52
α-helix	220-222	3
β-strand	225-226	2	58
β-strand	232	1	59
α-helix	238-243	6
β-strand	247	1	59
β-strand	252	1	60
β-strand	253	1	61
α-helix	263-272	10
β-strand	277	1	62
β-strand	278-285	8	53
α-helix	288-296	9
β-strand	301-302	2	63
β-strand	309-310	2	63
α-helix	311-314	4
β-strand	315-321	7	53
α-helix	328-345	18
β-strand	349	1	64
β-strand	350	1	62
β-strand	353	1	53
α-helix	357-371	15
α-helix	377-379	3
α-helix	384-393	10
β-strand	398-399	2	58
β-strand	407-408	2	58
β-strand	409	1	64
β-strand	413	1	60
α-helix	426-432	7
β-strand	438	1	61
α-helix	444-447	4
β-strand	460	1	61
α-helix	468-474	7
α-helix	478-502	25
α-helix	504-506	3
α-helix	509-524	16
α-helix	540-564	25
α-helix	567-574	8
α-helix	576-583	8
α-helix	584-586	3
α-helix	588	1
α-helix	595-613	19

Chain F: 23 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	17-19	3
β-strand	27-28	2	3
β-strand	34-35	2	5
β-strand	38-40	3	5
β-strand	48	1	51
β-strand	52-54	3	5
β-strand	64-71	8	5
β-strand	74-79	6	5
β-strand	93-94	2	3
β-strand	95	1	5
β-strand	101-104	4	65
α-helix	106-108	3
β-strand	112-113	2	66
β-strand	119	1	66
α-helix	124-126	3
β-strand	130-133	4	65
β-strand	139	1	54
α-helix	141-143	3
β-strand	144-145	2	67
β-strand	150-151	2	68
α-helix	156-161	6
β-strand	164-165	2	68
β-strand	169	1	69
β-strand	172	1	70
β-strand	175	1	71
α-helix	180-189	10
β-strand	193	1	68
β-strand	208-210	3	72
β-strand	213-217	5	66
α-helix	219-231	13
α-helix	235-237	3
β-strand	238	1	72
β-strand	240-244	5	66
α-helix	250-254	5
α-helix	255-269	15
β-strand	273-275	3	72
β-strand	276	1	69
β-strand	278-279	2	66
α-helix	281-293	13
α-helix	297-298	2
β-strand	299	1	73
β-strand	305	1	73
α-helix	308-316	9
β-strand	321-322	2	67
β-strand	328	1	72
β-strand	331	1	69
β-strand	334	1	70
β-strand	337	1	71
α-helix	345-353	9
β-strand	357	1	74
β-strand	358	1	70
α-helix	363-366	4
β-strand	379	1	74
α-helix	383-386	4
α-helix	395-420	26
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	478-480	3
α-helix	481-485	5

Chain G: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	12-110	99
α-helix	114-132	19
β-strand	138-140	3	3
α-helix	146-163	18
β-strand	173-174	2	3
β-strand	188-191	4	3
β-strand	197-201	5	3
α-helix	203-210	8
α-helix	215-222	8

Chain H: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	4-6	3
α-helix	7-62	56
α-helix	64-75	12
α-helix	78-89	12
α-helix	92-103	12

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
V-type proton ATPase subunit C	O	protein	392	Saccharomyces cerevisiae S288C	P31412 (AlphaFold model)
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae S288C	P22203 (AlphaFold model)
V-type proton ATPase subunit G	H, J, L	protein	122	Saccharomyces cerevisiae S288C	P48836 (AlphaFold model)
Yeast Vacuolar ATPase A subunit	A, C, E	protein	617	Saccharomyces cerevisiae S288C	P17255 (AlphaFold model)
V-type proton ATPase subunit B	B, D, F	protein	517	Saccharomyces cerevisiae S288C	P16140
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae S288C	P32610
V-type proton ATPase subunit F	N	protein	118	Saccharomyces cerevisiae S288C	P39111
Oxidation resistance protein 1	P	protein	273	Saccharomyces cerevisiae S288C	Q08952

Sequence of entity 1 (O), FASTA

>7FDE_1 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 2 (G, I, K), FASTA

>7FDE_2 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 3 (H, J, L), FASTA

>7FDE_3 V-type proton ATPase subunit G (chains H, J, L)
MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDK
ELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHIN
AL

Sequence of entity 4 (A, C, E), FASTA

>7FDE_4 Yeast Vacuolar ATPase A subunit (chains A, C, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTD

Sequence of entity 5 (B, D, F), FASTA

>7FDE_5 V-type proton ATPase subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Sequence of entity 6 (M), FASTA

>7FDE_6 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 7 (N), FASTA

>7FDE_7 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 8 (P), FASTA

>7FDE_8 Oxidation resistance protein 1 (chains P)
MFGVKDAIFKIKRSIAGTDSSDSTAYTTASESSPQLKDSHNPFRNKTTSERTIVEEGSLP
PVRLNGYLPSTKNKLLTPEMCDEIRTLMPTRIQLYTEWNLLYSLEQHGSSLHSLYSNVAP
DSKEFRRVGYVLVIKDRKNGIFGAYSNEAFHPNEHRQYTGNGECFLWKLDKVPDVNISEK
EESEQEGKEGKEEGDKEERWRFSGYPYTGVNEFAIYCTSEFLSMGAGDGHYGLLCDDGLL
HGVSNPCQTYGNEVLSKEGKKFSIVALEVWRVG

Primary citation

CryoEM Structures of Reconstituted V-ATPase and Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Khan, M.M., Lee, S., Oot, R.A. et al. EMBO J (2021).

Other PDB entries of the same protein (UniProt P31412 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U7L 1.75 Å, Crystal Structure of subunit C (vma5p) of the yeast V-ATPase
4EFA 2.82 Å, Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast…
4DL0 2.9 Å, Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast…
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae
7TMR 3.5 Å, V-ATPase from Saccharomyces cerevisiae, State 1
9MOY 3.6 Å, Reconstituted yeast V-ATPase bound to Rtc5p
9ODU 3.9 Å, Yeast V-ATPase bound to Rtc5p, rotary state 2
7FDA 4.2 Å, CryoEM Structure of Reconstituted V-ATPase, state1
7FDB 4.8 Å, CryoEM Structures of Reconstituted V-ATPase,State2
6O7V 6.6 Å, Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1
7FDC 6.6 Å, CryoEM Structures of Reconstituted V-ATPase, state3
5VOX 6.8 Å, Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1)

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