9VPB: IF1 bound bovine F-ATP synthase planar dimer

Cryo-EM structure of the IF1 bound bovine F-ATP synthase planar dimer. Determined by electron microscopy at 5.0 Å resolution. Released 1 Jul 2026.

Method: Electron microscopy
Resolution: 5.0 Å
Organism: Bos taurus
Chains: 54
Atoms: 49,792
Mol. weight: 1367.65 kDa
Released: 1 Jul 2026

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

Secondary structure: helices and β-sheets

9VPB contains 533 α-helices and 352 β-strands across 54 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.

Chains 8 and A8: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-4	3
α-helix	6-17	12
α-helix	18-24	7
α-helix	25-29	5
α-helix	34-37	4

Chains a and Aa: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	19-25	7
α-helix	26-30	5
α-helix	41-58	18
α-helix	63-66	4
α-helix	69-86	18
α-helix	94-96	3
α-helix	98-119	22
α-helix	122-126	5
α-helix	135-137	3
α-helix	138-181	44
α-helix	186-224	39

Chains A and AA: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
β-strand	28-35	8	2
β-strand	38-43	6	2
α-helix	47	1
β-strand	48	1	3
β-strand	51-55	5	2
β-strand	60-66	7	2
β-strand	71-75	5	2
α-helix	79-81	3
β-strand	87-94	8	2
β-strand	96-99	4	4
α-helix	101-103	3
β-strand	107-109	3	5
β-strand	114	1	5
β-strand	125-128	4	4
α-helix	131-134	4
β-strand	139	1	6
β-strand	145	1	7
α-helix	151-156	6
β-strand	160	1	7
β-strand	164	1	5
β-strand	166-169	4	8
α-helix	175-185	11
α-helix	187-190	4
α-helix	195-197	3
β-strand	200-206	7	5
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	5
α-helix	240-259	20
β-strand	263-269	7	5
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-306	9
β-strand	310-311	2	5
β-strand	312	1	6
α-helix	314-316	3
β-strand	320-325	6	5
β-strand	326-328	3	8
α-helix	337-345	9
β-strand	348-352	5	8
α-helix	354-359	6
β-strand	365	1	8
β-strand	371-372	2	8
α-helix	381-400	20
α-helix	401-403	3
α-helix	412-427	16
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-475	15
α-helix	477-486	10
α-helix	491-507	17

Chains Ab and b: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	4-6	3
α-helix	20-24	5
α-helix	34-37	4
α-helix	39-42	4
α-helix	46-48	3
α-helix	54-56	3
α-helix	62-70	9
α-helix	71-75	5
α-helix	76-110	35
α-helix	112-118	7
α-helix	122-126	5
α-helix	129-168	40
α-helix	169-171	3
α-helix	177-183	7
α-helix	192-206	15

Chains AB and B: 28 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
α-helix	19-21	3
β-strand	28-35	8	9
β-strand	38-43	6	9
α-helix	47	1
β-strand	48	1	23
β-strand	51	1	24
β-strand	52-54	3	9
β-strand	60-66	7	9
β-strand	71-75	5	9
α-helix	79-81	3
β-strand	87-89	3	9
β-strand	94	1	24
β-strand	96-99	4	25
α-helix	101-103	3
β-strand	107-109	3	26
β-strand	114	1	26
β-strand	125-128	4	25
α-helix	131-134	4
β-strand	139	1	27
β-strand	145	1	28
α-helix	151-156	6
β-strand	160	1	28
β-strand	164	1	26
β-strand	166-169	4	29
α-helix	175-185	11
α-helix	187-190	4
α-helix	195-197	3
β-strand	200-206	7	26
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	26
α-helix	240-259	20
β-strand	263-269	7	26
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-306	9
β-strand	310-311	2	26
β-strand	312	1	27
α-helix	314-316	3
β-strand	320-325	6	26
β-strand	326-328	3	29
α-helix	337-345	9
β-strand	348-352	5	29
α-helix	354-359	6
β-strand	365	1	29
β-strand	371-372	2	29
α-helix	381-400	20
α-helix	401-403	3
α-helix	412-427	16
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-475	15
α-helix	477-486	10
α-helix	491-507	17

Chains AC and C: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	28-35	8	9
β-strand	38-42	5	9
β-strand	48	1	36
β-strand	51-55	5	9
β-strand	60-66	7	9
β-strand	70-75	6	9
β-strand	87-94	8	9
β-strand	96-99	4	37
α-helix	101-103	3
β-strand	107-109	3	38
β-strand	114	1	38
β-strand	125-128	4	37
α-helix	131-134	4
β-strand	139	1	39
β-strand	145	1	40
α-helix	151-156	6
β-strand	160	1	40
β-strand	164	1	38
β-strand	166-169	4	41
α-helix	175-185	11
α-helix	187-190	4
α-helix	195-197	3
β-strand	200-206	7	38
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	38
α-helix	240-259	20
β-strand	263-269	7	38
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-306	9
β-strand	310-311	2	38
β-strand	312	1	39
α-helix	314-316	3
β-strand	320-325	6	38
β-strand	326-328	3	41
α-helix	337-345	9
β-strand	348-352	5	41
α-helix	354-359	6
β-strand	365	1	41
β-strand	371-372	2	41
α-helix	381-400	20
α-helix	401-403	3
α-helix	412-427	16
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-475	15
α-helix	477-486	10
α-helix	491-507	17

Chains Ad and d: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	24-43	20
α-helix	53-59	7
α-helix	65-75	11
α-helix	89-96	8
α-helix	97-101	5
α-helix	104-122	19
α-helix	125-126	2
α-helix	127-129	3
α-helix	132-138	7
α-helix	140-142	3

Chains AD and D: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	9
β-strand	24-28	5	9
α-helix	32-35	4
β-strand	38-42	5	9
β-strand	49-56	8	9
β-strand	61-66	6	9
β-strand	74	1	36
β-strand	78-85	8	9
β-strand	87-90	4	48
β-strand	99	1	49
β-strand	105	1	49
β-strand	116-119	4	48
α-helix	124-126	3
α-helix	127-129	3
β-strand	130	1	50
β-strand	136-137	2	51
α-helix	142-147	6
α-helix	149	1
β-strand	150-151	2	51
β-strand	156-158	3	52
α-helix	166-173	8
α-helix	174-178	5
β-strand	185-190	6	52
α-helix	195-207	13
β-strand	219-224	6	52
α-helix	230-232	3
α-helix	236-249	14
β-strand	254-260	7	52
α-helix	264-273	10
α-helix	274-276	3
α-helix	289-297	9
β-strand	303	1	50
β-strand	307-313	7	52
α-helix	317-319	3
α-helix	324-329	6
α-helix	330-332	3
β-strand	335-336	2	52
β-strand	339	1	53
α-helix	341-344	4
β-strand	352	1	53
β-strand	358	1	52
α-helix	364-392	29
α-helix	404-417	14
α-helix	424-426	3
α-helix	438-450	13
α-helix	458-460	3
α-helix	467-479	13

19 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
ATP synthase F(0) complex subunit 8	8, A8	protein	66	Bos taurus	P03929 (AlphaFold model)
ATP synthase subunit alpha	A, AA, AB, AC, B, C	protein	553	Bos taurus	F1MLB8 (AlphaFold model)
ATP synthase F(1) complex catalytic subunit beta, mitochondrial	AD, AE, AF, D, E, F	protein	528	Bos taurus	P00829 (AlphaFold model)
ATP synthase F(1) complex subunit gamma, mitochondrial	AG, G	protein	298	Bos taurus	P05631 (AlphaFold model)
ATP synthase F(1) complex subunit delta, mitochondrial	AH, H	protein	168	Bos taurus	P05630
ATP synthase F(1) complex subunit epsilon, mitochondrial	AI, I	protein	51	Bos taurus	P05632
ATPase inhibitor, mitochondrial	AJ, J	protein	109	Bos taurus	P01096
ATP synthase F(0) complex subunit C2, mitochondrial	AK, AL, AM, AN, AO, AP, AQ, AR, K, L, M, N, O, P, Q, R	protein	143	Bos taurus	P07926
ATP synthase peripheral stalk subunit OSCP, mitochondrial	AS, S	protein	213	Bos taurus	P13621
ATP synthase F(0) complex subunit a	Aa, a	protein	226	Bos taurus	P00847
ATP synthase peripheral stalk subunit b, mitochondrial	Ab, b	protein	256	Bos taurus	P13619
ATP synthase peripheral stalk subunit d, mitochondrial	Ad, d	protein	161	Bos taurus	P13620

4 more molecules are not listed.

Sequence of entity 1 (8, A8), FASTA

>9VPB_1 ATP synthase F(0) complex subunit 8 (chains 8, A8)
MPQLDTSTWLTMILSMFLTLFIIFQLKVSKHNFYHNPELTPTKMLKQNTPWETKWTKIYL
PLLLPL

Sequence of entity 2 (A, AA, AB, AC, B, C), FASTA

>9VPB_2 ATP synthase subunit alpha (chains A, AA, AB, AC, B, C)
MLSVRVAAAVARALPRRAGLVSKNALGSSFIAARNLHASNSRLQKTGTAEVSSILEERIL
GADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFG
NDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGII
PRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKK
KLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYF
RDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFG
GGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSA
AQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMA
IEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKL
KEIVTNFLAGFEA

Sequence of entity 3 (AD, AE, AF, D, E, F), FASTA

>9VPB_3 ATP synthase F(1) complex catalytic subunit beta, mitochondrial (chains AD, AE, AF, D, E, F)
MLGLVGRVVAASASGALRGLSPSAPLPQAQLLLRAAPAALQPARDYAAQASPSPKAGATT
GRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLV
RGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSVEQ
EILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERT
REGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQD
VLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAI
YVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDV
ARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLGK
LVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHS

Sequence of entity 4 (AG, G), FASTA

>9VPB_4 ATP synthase F(1) complex subunit gamma, mitochondrial (chains AG, G)
MFSRAGVAGLSAWTVQPQWIQVRNMATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAE
RELKPARVYGVGSLALYEKADIKTPEDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAAN
LAAAGKEVKIIGVGDKIRSILHRTHSDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEF
DEGSIIFNRFRSVISYKTEEKPIFSLDTISSAESMSIYDDIDADVLRNYQEYSLANIIYY
SLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Sequence of entity 5 (AH, H), FASTA

>9VPB_5 ATP synthase F(1) complex subunit delta, mitochondrial (chains AH, H)
MLPSALLRRPGLGRLVRQVRLYAEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDV
PTQTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAV
TLDMLDLGAAKANLEKAQSELLGAADEATRAEIQIRIEANEALVKALE

Sequence of entity 6 (AI, I), FASTA

>9VPB_6 ATP synthase F(1) complex subunit epsilon, mitochondrial (chains AI, I)
MVAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE

Sequence of entity 7 (AJ, J), FASTA

>9VPB_7 ATPase inhibitor, mitochondrial (chains AJ, J)
MAATALAARTRQAVWSVWAMQGRGFGSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFR
ARAKEQLAALKKHHENEISHHAKEIERLQKEIERHKQSIKKLKQSEDDD

Sequence of entity 8 (AK, AL, AM, AN, AO, AP, AQ, AR, K, L, M, N, O, P, Q, R), FASTA

>9VPB_8 ATP synthase F(0) complex subunit C2, mitochondrial (chains AK, AL, AM, AN, AO, AP, AQ, AR, K, L, M, N, O, P, Q, R)
MYTCAKFVSTPSLIRRTSTVLSRSLSAVVVRRPETLTDESHSSLAVVPRPLTTSLTPSRS
FQTSAISRDIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAIL
GFALSEAMGLFCLMVAFLILFAM

Sequence of entity 9 (AS, S), FASTA

>9VPB_9 ATP synthase peripheral stalk subunit OSCP, mitochondrial (chains AS, S)
MAALAVSGLSQQVRCFSTSVVRPFAKLVRPPVQIYGIEGRYATALYSAASKQNKLEQVEK
ELLRVGQILKEPKMAASLLNPYVKRSVKVKSLSDMTAKEKFSPLTSNLINLLAENGRLTN
TPAVISAFSTMMSVHRGEVPCTVTTASALDEATLTELKTVLKSFLSKGQVLKLEVKIDPS
IMGGMIVRIGEKYVDMSAKTKIQKLSRAMREIL

Sequence of entity 10 (Aa, a), FASTA

>9VPB_10 ATP synthase F(0) complex subunit a (chains Aa, a)
MNENLFTSFITPVILGLPLVTLIVLFPSLLFPTSNRLVSNRFVTLQQWMLQLVSKQMMSI
HNSKGQTWTLMLMSLILFIGSTNLLGLLPHSFTPTTQLSMNLGMAIPLWAGAVITGFRNK
TKASLAHFLPQGTPTPLIPMLVIIETISLFIQPMALAVRLTANITAGHLLIHLIGGATLA
LMSISTTTALITFTILILLTILEFAVAMIQAYVFTLLVSLYLHDNT

Sequence of entity 11 (Ab, b), FASTA

>9VPB_11 ATP synthase peripheral stalk subunit b, mitochondrial (chains Ab, b)
MLSRVVLSAAAAAAPSLKNAALLGPGVLQATRIFHTGQPSLAPVPPLPEHGGKVRFGLIP
EEFFQFLYPKTGVTGPYVLGTGLILYLLSKEIYVITPETFSAISTIGFLVYIVKKYGASV
GEFADKLNEQKIAQLEEVKQASIKQIQDAIDMEKSQQALVQKRHYLFDVQRNNIAMALEV
TYRERLHRVYREVKNRLDYHISVQNMMRQKEQEHMINWVEKRVVQSISAQQEKETIAKCI
ADLKLLSKKAQAQPVM

Sequence of entity 12 (Ad, d), FASTA

>9VPB_12 ATP synthase peripheral stalk subunit d, mitochondrial (chains Ad, d)
MAGRKLALKTIDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKAN
VAKAGLVDDFEKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKELE
KMRNIIPFDQMTIEDLNEVFPETKLDKKKYPYWPHRPIETL

Primary citation

A planar dimer of bovine ATP synthase. Jiko, C., Nakano, A., Teshirogi, Y. et al. Cell Death Differ (2026). DOI 10.1038/s41418-026-01797-4 · PubMed

Other PDB entries of the same protein (UniProt P03929 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ZQM 3.29 Å, bovine ATP synthase monomer state 2 (combined)
9W2R 3.4 Å, Cryo-EM structure of FoF1-ATPase monomer state 1 on the bovine heart submitochondrial…
6ZIT 3.49 Å, bovine ATP synthase Stator domain, state 2
6ZBB 3.61 Å, bovine ATP synthase Fo domain
6ZPO 4.0 Å, bovine ATP synthase monomer state 1 (combined)
6ZQN 4.0 Å, bovine ATP synthase monomer state 3 (combined)
9W2S 4.0 Å, Cryo-EM structure of FoF1-ATPase monomer state 3 on the bovine heart submitochondrial…
9W2T 4.1 Å, Cryo-EM structure of Fo domain of FoF1-ATPase monomer state on the bovine heart…
6ZIQ 4.33 Å, bovine ATP synthase stator domain, state 1
6ZIU 6.02 Å, bovine ATP synthase stator domain, state 3
9VPC 7.2 Å, Cryo-EM structure of the IF1 bound bovine ATP synthase tetramer
7AJF 8.45 Å, bovine ATP synthase dimer state2:state2

Browse structure collections

About this viewer

MolViewer shows 9VPB 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.