9NN1: Yeast V1-ATPase

Yeast V1-ATPase bound to Rtc5p. Determined by electron microscopy at 3.7 Å resolution. Released 4 Mar 2026.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Saccharomyces cerevisiae
Chains: 15
Atoms: 38,832
Mol. weight: 605.08 kDa
Ligands: ADP
Released: 4 Mar 2026

Explore 9NN1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NN1 contains 235 α-helices and 257 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: 26 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
β-strand	48-51	4	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	2
β-strand	84-87	4	1
β-strand	93-96	4	3
β-strand	104-105	2	4
β-strand	111	1	4
α-helix	112-119	8
β-strand	123	1	5
β-strand	139-143	5	6
β-strand	151-153	3	7
β-strand	157-161	5	6
β-strand	170-173	4	6
β-strand	179-185	7	7
α-helix	186-187	2
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	238-243	6
β-strand	247	1	9
β-strand	251-255	5	4
α-helix	263-272	10
β-strand	277-285	9	4
α-helix	287-296	10
α-helix	297-299	3
β-strand	301-302	2	10
β-strand	309-310	2	10
α-helix	311-314	4
β-strand	315-321	7	4
α-helix	326-345	20
β-strand	349-355	7	4
α-helix	357-370	14
α-helix	373-375	3
β-strand	376	1	11
β-strand	380	1	11
α-helix	384-393	10
β-strand	398-399	2	8
α-helix	400-401	2
β-strand	407-408	2	8
β-strand	409-416	8	4
α-helix	426-434	9
β-strand	437-438	2	4
β-strand	441	1	12
α-helix	443-446	4
β-strand	454	1	12
β-strand	460-461	2	4
α-helix	468-474	7
α-helix	478-502	25
α-helix	504-506	3
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	593-613	21

Chain B: 25 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	13-17	5
β-strand	26-28	3	1
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	2
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	87	1	13
β-strand	92-95	4	1
β-strand	101-104	4	45
α-helix	106-108	3
β-strand	112-113	2	46
β-strand	119	1	46
α-helix	124-126	3
β-strand	130-133	4	45
α-helix	138	1
β-strand	139	1	5
α-helix	140	1
α-helix	141-143	3
β-strand	144	1	47
β-strand	150-151	2	48
β-strand	152	1	49
α-helix	156-159	4
β-strand	164-165	2	48
β-strand	169	1	46
β-strand	172-174	3	50
α-helix	180-190	11
β-strand	192	1	49
β-strand	208-217	10	46
α-helix	219-231	13
α-helix	235-237	3
β-strand	238-244	7	46
α-helix	249-270	22
β-strand	273-278	6	46
α-helix	281-294	14
β-strand	299	1	51
α-helix	301-303	3
β-strand	305	1	51
α-helix	308-316	9
β-strand	320-321	2	46
β-strand	322	1	47
β-strand	328-333	6	46
β-strand	334-336	3	50
α-helix	345-353	9
β-strand	356-360	5	50
α-helix	362-366	5
β-strand	373-380	8	50
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 C: 24 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	1
β-strand	34-38	5	1
β-strand	44	1	13
β-strand	47-51	5	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	14
β-strand	85-91	7	1
β-strand	93-96	4	15
β-strand	103-105	3	16
β-strand	111	1	16
α-helix	112-118	7
β-strand	123	1	17
α-helix	124-125	2
β-strand	139-143	5	18
β-strand	151-153	3	19
β-strand	157-162	6	18
β-strand	170-173	4	18
α-helix	174-175	2
β-strand	179-185	7	19
β-strand	189-191	3	18
β-strand	196-202	7	19
β-strand	205-210	6	19
β-strand	213-216	4	15
α-helix	220-222	3
β-strand	225-227	3	16
β-strand	232	1	20
α-helix	238-243	6
β-strand	247	1	20
β-strand	251-255	5	16
α-helix	262-271	10
β-strand	277-285	9	16
α-helix	287-296	10
α-helix	297-299	3
β-strand	301-303	3	21
β-strand	308-310	3	21
α-helix	311-314	4
β-strand	315-321	7	16
α-helix	326-345	20
β-strand	349-354	6	16
α-helix	357-371	15
β-strand	377	1	22
β-strand	380	1	22
α-helix	384-392	9
β-strand	396-399	4	16
α-helix	400	1
β-strand	407-416	10	16
α-helix	426-432	7
β-strand	437-438	2	16
β-strand	441	1	23
α-helix	443-448	6
β-strand	454	1	23
β-strand	460-461	2	16
α-helix	464-474	11
α-helix	478-502	25
α-helix	509-524	16
α-helix	540-562	23
α-helix	567-572	6
α-helix	575-583	9
α-helix	584-586	3
α-helix	589-591	3
α-helix	593-614	22

Chain D: 23 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	10-19	10
β-strand	27-28	2	1
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	14
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	87	1	24
β-strand	92-95	4	1
β-strand	101-104	4	52
α-helix	106-108	3
β-strand	111-114	4	53
β-strand	119	1	53
α-helix	124-126	3
β-strand	130-133	4	52
α-helix	138	1
β-strand	139	1	17
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	54
β-strand	150	1	55
β-strand	151-152	2	56
α-helix	156-159	4
β-strand	165	1	55
β-strand	169	1	53
β-strand	172-174	3	57
α-helix	180-190	11
β-strand	192-193	2	56
β-strand	208-217	10	53
α-helix	219-232	14
α-helix	234-237	4
β-strand	238-244	7	53
α-helix	249-268	20
β-strand	273-278	6	53
α-helix	281-294	14
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	54
β-strand	328-331	4	53
β-strand	334-336	3	57
α-helix	345-352	8
β-strand	356-357	2	59
β-strand	358-359	2	57
β-strand	360	1	60
α-helix	362-366	5
β-strand	373	1	60
β-strand	379-380	2	59
α-helix	381-385	5
β-strand	389	1	61
β-strand	392	1	61
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	478-483	6

Chain E: 24 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
β-strand	44	1	24
β-strand	48-51	4	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	25
β-strand	84-87	4	1
β-strand	93-96	4	26
β-strand	104-105	2	27
β-strand	111	1	27
α-helix	112-119	8
β-strand	123	1	28
β-strand	139-143	5	29
β-strand	151-153	3	30
β-strand	157-161	5	29
β-strand	170-173	4	29
α-helix	174-175	2
β-strand	179-185	7	30
β-strand	189-191	3	29
β-strand	198-202	5	30
β-strand	205-209	5	30
β-strand	213-216	4	26
α-helix	220-222	3
β-strand	225-227	3	27
β-strand	232	1	31
α-helix	238-243	6
β-strand	247	1	31
β-strand	251-255	5	27
α-helix	262-272	11
β-strand	277-285	9	27
α-helix	287-296	10
α-helix	297-299	3
β-strand	302	1	32
β-strand	308	1	32
α-helix	310	1
α-helix	311-314	4
β-strand	315-321	7	27
α-helix	328-345	18
β-strand	349-354	6	27
α-helix	358-370	13
β-strand	375-376	2	33
β-strand	380-381	2	33
α-helix	384-392	9
β-strand	396-399	4	27
β-strand	407-416	10	27
α-helix	426-432	7
β-strand	437-438	2	27
β-strand	441	1	34
α-helix	443-447	5
β-strand	454	1	34
β-strand	460-461	2	27
α-helix	468-474	7
α-helix	478-499	22
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	593-613	21

Chain F: 27 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	10-17	8
α-helix	18-20	3
β-strand	26-28	3	1
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	25
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	92-95	4	1
β-strand	101-104	4	62
α-helix	106-108	3
β-strand	111-114	4	63
β-strand	119	1	63
β-strand	130-133	4	62
α-helix	136-138	3
β-strand	139	1	28
α-helix	140	1
α-helix	141-143	3
β-strand	144	1	64
β-strand	150-152	3	65
α-helix	156-161	6
β-strand	164-165	2	65
β-strand	172-174	3	66
α-helix	180-190	11
β-strand	192-193	2	65
β-strand	209-213	5	63
β-strand	217	1	67
α-helix	219-231	13
α-helix	235-237	3
β-strand	238-242	5	63
β-strand	244	1	67
α-helix	249-253	5
α-helix	255-270	16
β-strand	274-278	5	63
α-helix	281-295	15
α-helix	297-298	2
β-strand	299	1	68
α-helix	301-303	3
β-strand	305	1	68
α-helix	308-316	9
β-strand	320-321	2	63
β-strand	322	1	64
β-strand	328-331	4	63
β-strand	334-336	3	66
α-helix	345-353	9
β-strand	358-359	2	66
β-strand	360	1	69
α-helix	362-366	5
β-strand	373	1	69
α-helix	383-386	4
α-helix	396-420	25
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
α-helix	487-488	2

Chain G: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	71-73	3
α-helix	74-110	37
α-helix	114-132	19
β-strand	136-142	7	1
α-helix	143-145	3
α-helix	146-163	18
α-helix	167-169	3
β-strand	171-179	9	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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	66-88	23
α-helix	91-103	13
α-helix	108-110	3

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	617	Saccharomyces cerevisiae	P17255 (AlphaFold model)
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae	P22203 (AlphaFold model)
Yeast V-ATPase subunit G	H, J, L	protein	122	Saccharomyces cerevisiae	P48836 (AlphaFold model)
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae	P32610 (AlphaFold model)
V-type proton ATPase subunit F	N	protein	118	Saccharomyces cerevisiae	P39111
Restriction of telomere capping protein 5	R	protein	567	Saccharomyces cerevisiae	Q12108
V-type proton ATPase subunit B	B, D, F	protein	517	Saccharomyces cerevisiae	P16140

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

>9NN1_1 H(+)-transporting two-sector ATPase (chains A, C, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTD

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

>9NN1_2 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

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

>9NN1_3 Yeast V-ATPase subunit G (chains H, J, L)
MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDK
ELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHIN
AL

Sequence of entity 4 (M), FASTA

>9NN1_4 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 5 (N), FASTA

>9NN1_5 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 6 (R), FASTA

>9NN1_6 Restriction of telomere capping protein 5 (chains R)
MGQSSSISSSNEEGSSHSKKFTNSKDILAYFNNKAQQQVTIPELVSFKGNLQIEDLNTPI
SHKALCNSLYFPQNHAMIVGIVTNMLRVLSNFPLMKSSYEPITGYGLLKCILLLNRARCA
KFLKTKSYDQLKLLFISLSLQKTDKEELSEESENDGNKELTIKQIITGFDDVDTEMLCIP
ADFMLQFLTWLLILTVDCPTTNSKLDNTETHDQWGNFKVSALNLLRTMNPDVVGDIESHS
ITFQQFSTAIRTVMPNLLKPLENLMEHFFYLQHDLVDHDTNLSSIQDSKVMTPALLAQLS
TGLPKELFIHKLQSLYIGRKSGFSMRSLQAKVFKWMAPSILVVSGMRITNSEEYAAEKNP
RYRHFLEEFPKLKESDQMMDASHLNKRKTTFAVYIDDPWKVTNKDYFGDLNTRIIEISPR
QDIYKVNQKGTIYFNTIGGGIGIGDKQPLIKPASKRYIPGNVSLTFDSTLEFAVFRNTGY
GGSLDPGLLSMERKEENSPYELHFLIQDVEVWGCGGEKELEEQIKQLEWEEAESKRRQQI
NLRSLGEDRALLEMAGLVGQHQGGGSM

Sequence of entity 7 (B, D, F), FASTA

>9NN1_7 V-type proton ATPase subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

TLDc Protein Rtc5p Assembles Yeast V-ATPase. Khan, M.M., Wilkens, S. To be published.

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…

Browse structure collections

About this viewer

MolViewer shows 9NN1 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.