9VPD: PDB entry 9VPD

Cryo-EM structure of the IF1 bound bovine ATP synthase monomer: rotary state 1, F1 focused map. Determined by electron microscopy at 2.3 Å resolution. Released 1 Jul 2026.

Method: Electron microscopy
Resolution: 2.3 Å
Organism: Bos taurus
Chains: 14
Atoms: 27,808
Mol. weight: 503.68 kDa
Ligands: ADP, MG, ATP
Released: 1 Jul 2026

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

Secondary structure: helices and β-sheets

9VPD contains 170 α-helices and 185 β-strands across 14 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: 22 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
β-strand	28-35	8	1
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	2
β-strand	51-55	5	1
β-strand	60-66	7	1
β-strand	71-75	5	1
β-strand	87-94	8	1
β-strand	96-99	4	3
α-helix	101-103	3
β-strand	107-109	3	4
β-strand	114	1	4
β-strand	125-128	4	3
β-strand	139	1	5
β-strand	145	1	6
α-helix	151-156	6
β-strand	160	1	6
β-strand	164	1	4
β-strand	167-169	3	7
α-helix	175-185	11
α-helix	187-191	5
β-strand	200-206	7	4
α-helix	210-222	13
β-strand	229-234	6	4
α-helix	240-259	20
β-strand	263-269	7	4
α-helix	271-284	14
α-helix	287-288	2
β-strand	289	1	8
α-helix	291-293	3
β-strand	295	1	8
α-helix	299-306	8
β-strand	311	1	4
β-strand	312	1	5
β-strand	320-323	4	4
β-strand	326-328	3	7
α-helix	337-345	9
β-strand	348-349	2	9
β-strand	350-351	2	7
β-strand	352	1	10
α-helix	355-358	4
β-strand	365	1	10
β-strand	367	1	11
β-strand	370	1	11
β-strand	371-372	2	9
α-helix	375-378	4
α-helix	381-398	18
α-helix	402-405	4
α-helix	412-428	17
α-helix	438-449	12
α-helix	458-474	17
α-helix	477-486	10
α-helix	491-505	15

Chain b: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	110-118	9
α-helix	123-184	62
α-helix	190-208	19

Chain B: 21 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	12
β-strand	38-43	6	12
α-helix	47	1
β-strand	48	1	13
β-strand	51-55	5	12
β-strand	60-66	7	12
β-strand	71-75	5	12
α-helix	79-81	3
β-strand	87-94	8	12
β-strand	96-99	4	14
α-helix	101-103	3
β-strand	107-108	2	15
β-strand	114	1	15
β-strand	125-128	4	14
α-helix	131-134	4
β-strand	139	1	16
β-strand	145	1	17
α-helix	151-156	6
β-strand	160	1	17
β-strand	164	1	15
β-strand	167-169	3	15
α-helix	175-185	11
α-helix	187-190	4
β-strand	199-206	8	15
α-helix	210-222	13
β-strand	229-234	6	15
α-helix	240-259	20
β-strand	263-269	7	15
α-helix	271-284	14
α-helix	291-293	3
α-helix	298-306	9
β-strand	311	1	15
β-strand	312	1	16
β-strand	320-323	4	15
β-strand	326-328	3	15
β-strand	330	1	18
β-strand	333	1	18
α-helix	337-345	9
β-strand	348	1	19
β-strand	352	1	20
α-helix	354-359	6
β-strand	365	1	20
β-strand	372	1	19
α-helix	375-377	3
α-helix	381-398	18
α-helix	412-427	16
α-helix	438-449	12
α-helix	461-474	14
α-helix	477-486	10
α-helix	491-506	16

Chain C: 21 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-17	11
β-strand	26-27	2	21
β-strand	29-35	7	1
β-strand	38-43	6	1
β-strand	51-55	5	1
β-strand	60-66	7	1
β-strand	71-75	5	1
β-strand	88-94	7	1
β-strand	96-99	4	22
α-helix	101-103	3
β-strand	107-109	3	23
β-strand	114	1	23
β-strand	125-128	4	22
α-helix	132-134	3
β-strand	139	1	24
β-strand	145	1	25
α-helix	151-155	5
β-strand	160	1	25
β-strand	164	1	23
β-strand	167-169	3	23
α-helix	175-185	11
α-helix	187-191	5
β-strand	199-206	8	23
α-helix	210-222	13
β-strand	229-234	6	23
α-helix	240-258	19
β-strand	263-269	7	23
α-helix	271-284	14
α-helix	291-293	3
α-helix	298-306	9
β-strand	311	1	23
β-strand	312	1	24
α-helix	314-316	3
β-strand	320-323	4	23
β-strand	326-328	3	23
α-helix	337-345	9
β-strand	349	1	26
β-strand	350-351	2	23
β-strand	352	1	27
α-helix	354-358	5
β-strand	365	1	27
β-strand	371	1	26
α-helix	381-399	19
α-helix	412-428	17
α-helix	438-449	12
α-helix	453-455	3
α-helix	461-475	15
α-helix	477-486	10
α-helix	491-506	16

Chain d: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	15-17	3
α-helix	24-43	20
α-helix	53-57	5
α-helix	63-75	13
α-helix	85-88	4
α-helix	89-97	9
α-helix	98-102	5
α-helix	103-111	9

Chain D: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	1
β-strand	24-29	6	1
α-helix	32-35	4
β-strand	39-42	4	1
β-strand	50-58	9	1
β-strand	61-66	6	1
β-strand	78-81	4	1
β-strand	87-90	4	28
β-strand	99	1	29
β-strand	105	1	29
β-strand	116-119	4	28
α-helix	123-126	4
α-helix	127-129	3
β-strand	130	1	30
β-strand	136-137	2	31
α-helix	142-147	6
β-strand	150-151	2	31
β-strand	155-160	6	32
α-helix	166-173	8
α-helix	174-178	5
β-strand	186-190	5	32
α-helix	194-207	14
β-strand	220-224	5	32
α-helix	230-248	19
β-strand	254-260	7	32
α-helix	263-273	11
α-helix	274-276	3
α-helix	278-280	3
β-strand	281	1	33
β-strand	285	1	33
α-helix	289-297	9
β-strand	303	1	30
β-strand	307-315	9	32
α-helix	317-319	3
α-helix	324-329	6
α-helix	330-332	3
β-strand	335-336	2	32
β-strand	339	1	34
α-helix	341-344	4
β-strand	352	1	34
β-strand	358	1	32
α-helix	369-392	24
α-helix	397-399	3
α-helix	404-417	14
α-helix	426-429	4
α-helix	438-450	13
α-helix	458-461	4
α-helix	467-479	13

Chain E: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	1
β-strand	24-28	5	1
α-helix	33-35	3
β-strand	38-42	5	1
β-strand	50-58	9	1
β-strand	61-66	6	1
β-strand	74	1	2
β-strand	78-85	8	1
β-strand	87-89	3	35
α-helix	92-94	3
β-strand	99	1	36
β-strand	105	1	36
β-strand	117-119	3	35
α-helix	124-126	3
β-strand	137	1	37
α-helix	142-147	6
β-strand	150	1	37
β-strand	156-159	4	36
α-helix	166-179	14
β-strand	185-192	8	36
α-helix	194-207	14
β-strand	220-225	6	36
α-helix	230-233	4
α-helix	236-249	14
β-strand	254-259	6	36
α-helix	262-276	15
α-helix	289-297	9
β-strand	307-313	7	36
α-helix	317-319	3
α-helix	324-329	6
β-strand	335-338	4	36
β-strand	339	1	38
α-helix	341-344	4
β-strand	352	1	38
β-strand	358-359	2	36
α-helix	364-367	4
α-helix	369-395	27
α-helix	397-399	3
α-helix	402-418	17
α-helix	423-425	3
α-helix	426-429	4
α-helix	438-450	13
α-helix	458-461	4
α-helix	467-478	12

Chain F: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	12
β-strand	24-28	5	12
α-helix	32-34	3
β-strand	39-43	5	12
β-strand	50-56	7	12
β-strand	61-66	6	12
β-strand	74	1	13
β-strand	78-81	4	12
β-strand	87-89	3	39
α-helix	92-94	3
β-strand	98-99	2	40
β-strand	117-119	3	39
α-helix	122-125	4
β-strand	130	1	41
α-helix	142-146	5
β-strand	156-160	5	40
α-helix	166-179	14
β-strand	184-190	7	40
α-helix	194-206	13
β-strand	219-224	6	40
α-helix	230-234	5
α-helix	237-248	12
β-strand	254-260	7	40
α-helix	263-275	13
α-helix	289-297	9
β-strand	303	1	41
β-strand	307-315	9	40
α-helix	317-319	3
α-helix	324-329	6
α-helix	330-332	3
β-strand	335-336	2	40
β-strand	339	1	42
α-helix	341-345	5
β-strand	352	1	42
α-helix	370-394	25
α-helix	402-417	16
α-helix	426-429	4
α-helix	438-450	13
α-helix	458-460	3
α-helix	467-478	12

6 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(1) complex subunit alpha, mitochondrial	A, B, C	protein	553	Bos taurus	P19483 (AlphaFold model)
ATP synthase F(1) complex catalytic subunit beta, mitochondrial	D, E, F	protein	528	Bos taurus	P00829 (AlphaFold model)
ATP synthase F(1) complex subunit gamma, mitochondrial	G	protein	298	Bos taurus	P05631 (AlphaFold model)
ATP synthase F(1) complex subunit delta, mitochondrial	H	protein	168	Bos taurus	P05630 (AlphaFold model)
ATP synthase F(1) complex subunit epsilon, mitochondrial	I	protein	51	Bos taurus	P05632
ATPase inhibitor, mitochondrial	J	protein	109	Bos taurus	P01096
ATP synthase peripheral stalk subunit OSCP, mitochondrial	S	protein	213	Bos taurus	P13621
ATP synthase peripheral stalk subunit b, mitochondrial	b	protein	256	Bos taurus	P13619
ATP synthase peripheral stalk subunit d, mitochondrial	d	protein	161	Bos taurus	P13620
ATP synthase peripheral stalk subunit F6, mitochondrial	h	protein	108	Bos taurus	P02721

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

>9VPD_1 ATP synthase F(1) complex subunit alpha, mitochondrial (chains A, B, C)
MLSVRVAAAVARALPRRAGLVSKNALGSSFIAARNLHASNSRLQKTGTAEVSSILEERIL
GADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFG
NDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGII
PRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKK
KLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYF
RDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFG
GGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSA
AQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMA
IEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALLSKIRTDGKISEESDAKL
KEIVTNFLAGFEA

Sequence of entity 2 (D, E, F), FASTA

>9VPD_2 ATP synthase F(1) complex catalytic subunit beta, mitochondrial (chains D, E, F)
MLGLVGRVVAASASGALRGLSPSAPLPQAQLLLRAAPAALQPARDYAAQASPSPKAGATT
GRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLV
RGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSVEQ
EILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERT
REGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQD
VLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAI
YVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDV
ARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLGK
LVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHS

Sequence of entity 3 (G), FASTA

>9VPD_3 ATP synthase F(1) complex subunit gamma, mitochondrial (chains G)
MFSRAGVAGLSAWTVQPQWIQVRNMATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAE
RELKPARVYGVGSLALYEKADIKTPEDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAAN
LAAAGKEVKIIGVGDKIRSILHRTHSDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEF
DEGSIIFNRFRSVISYKTEEKPIFSLDTISSAESMSIYDDIDADVLRNYQEYSLANIIYY
SLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Sequence of entity 4 (H), FASTA

>9VPD_4 ATP synthase F(1) complex subunit delta, mitochondrial (chains H)
MLPSALLRRPGLGRLVRQVRLYAEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDV
PTQTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAV
TLDMLDLGAAKANLEKAQSELLGAADEATRAEIQIRIEANEALVKALE

Sequence of entity 5 (I), FASTA

>9VPD_5 ATP synthase F(1) complex subunit epsilon, mitochondrial (chains I)
MVAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE

Sequence of entity 6 (J), FASTA

>9VPD_6 ATPase inhibitor, mitochondrial (chains J)
MAATALAARTRQAVWSVWAMQGRGFGSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFR
ARAKEQLAALKKHHENEISHHAKEIERLQKEIERHKQSIKKLKQSEDDD

Sequence of entity 7 (S), FASTA

>9VPD_7 ATP synthase peripheral stalk subunit OSCP, mitochondrial (chains S)
MAALAVSGLSQQVRCFSTSVVRPFAKLVRPPVQIYGIEGRYATALYSAASKQNKLEQVEK
ELLRVGQILKEPKMAASLLNPYVKRSVKVKSLSDMTAKEKFSPLTSNLINLLAENGRLTN
TPAVISAFSTMMSVHRGEVPCTVTTASALDEATLTELKTVLKSFLSKGQVLKLEVKIDPS
IMGGMIVRIGEKYVDMSAKTKIQKLSRAMREIL

Sequence of entity 8 (b), FASTA

>9VPD_8 ATP synthase peripheral stalk subunit b, mitochondrial (chains b)
MLSRVVLSAAAAAAPSLKNAALLGPGVLQATRIFHTGQPSLAPVPPLPEHGGKVRFGLIP
EEFFQFLYPKTGVTGPYVLGTGLILYLLSKEIYVITPETFSAISTIGFLVYIVKKYGASV
GEFADKLNEQKIAQLEEVKQASIKQIQDAIDMEKSQQALVQKRHYLFDVQRNNIAMALEV
TYRERLHRVYREVKNRLDYHISVQNMMRQKEQEHMINWVEKRVVQSISAQQEKETIAKCI
ADLKLLSKKAQAQPVM

Sequence of entity 9 (d), FASTA

>9VPD_9 ATP synthase peripheral stalk subunit d, mitochondrial (chains d)
MAGRKLALKTIDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKAN
VAKAGLVDDFEKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKELE
KMRNIIPFDQMTIEDLNEVFPETKLDKKKYPYWPHRPIETL

Sequence of entity 10 (h), FASTA

>9VPD_10 ATP synthase peripheral stalk subunit F6, mitochondrial (chains h)
MILQRLFRLSSAVQSAISVSWRRNIGITAVAFNKELDPVQKLFVDKIREYRTKRQTSGGP
VDAGPEYQQDLDRELFKLKQMYGKADMNTFPNFTFEDPKFEVVEKPQS

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3
MG	Magnesium ion	Mg	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3

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 P19483 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2JDI 1.9 Å, Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase…
2CK3 1.95 Å, Azide inhibited bovine F1-ATPase
1H8E 2.0 Å, (ADP.AlF4)2(ADP.SO4) bovine F1-ATPase (all three catalytic sites occupied)
2V7Q 2.1 Å, The structure of F1-ATPase inhibited by I1-60HIS, a monomeric form of the inhibitor…
1W0J 2.2 Å, Beryllium fluoride inhibited bovine F1-ATPase
2JIZ 2.3 Å, The Structure of F1-ATPase inhibited by resveratrol.
1E79 2.4 Å, Bovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide)
2JJ2 2.4 Å, The Structure of F1-ATPase inhibited by quercetin.
1E1R 2.5 Å, Bovine mitochondrial F1-atpase inhibited by MG2+ADP and aluminium fluoride
4ASU 2.6 Å, F1-ATPase in which all three catalytic sites contain bound nucleotide, with magnesium…
1E1Q 2.61 Å, Bovine mitochondrial F1-atpase at 100K
2JJ1 2.7 Å, The Structure of F1-ATPase inhibited by piceatannol.

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