6YY0: ATP synthase subunit alpha, mitochondrial

bovine ATP synthase F1-peripheral stalk domain, state 1. Determined by electron microscopy at 3.23 Å resolution. Released 9 Sept 2020.

Method: Electron microscopy
Resolution: 3.23 Å
Organism: Bos taurus
Chains: 14
Atoms: 30,336
Mol. weight: 455.83 kDa
Ligands: ADP, MG, ATP
Released: 9 Sept 2020

Explore 6YY0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YY0 contains 173 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	75-77	3
α-helix	79-118	40
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: 11 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	103-122	20
α-helix	132-138	7
α-helix	140-142	3

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	458-460	3
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 subunit alpha, mitochondrial	A, B, C	protein	510	Bos taurus	P19483 (AlphaFold model)
ATP synthase subunit beta, mitochondrial	D, E, F	protein	482	Bos taurus	P00829 (AlphaFold model)
ATP synthase subunit gamma, mitochondrial	G	protein	273	Bos taurus	P05631 (AlphaFold model)
ATP synthase subunit delta, mitochondrial	H	protein	146	Bos taurus	P05630 (AlphaFold model)
ATP synthase subunit epsilon, mitochondrial	I	protein	50	Bos taurus	P05632
ATPase inhibitor, mitochondrial	J	protein	66	Bos taurus	P01096
ATP synthase subunit O, mitochondrial	S	protein	190	Bos taurus	P13621
ATP synthase F(0) complex subunit B1, mitochondrial	b	protein	214	Bos taurus	P13619
ATP synthase subunit d, mitochondrial	d	protein	160	Bos taurus	P13620
ATP synthase-coupling factor 6, mitochondrial	h	protein	76	Bos taurus	P02721

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

>6YY0_1 ATP synthase subunit alpha, mitochondrial (chains A, B, C)
EKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLK
GMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGP
IGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAA
PLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFY
LHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKG
IRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSR
GVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALL
GKIRTDGKISEESDAKLKEIVTNFLAGFEA

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

>6YY0_2 ATP synthase subunit beta, mitochondrial (chains D, E, F)
AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGES
TVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAI
HAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA
HGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTG
LTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERI
TTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSR
IMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQ
PFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEE
HS

Sequence of entity 3 (G), FASTA

>6YY0_3 ATP synthase subunit gamma, mitochondrial (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Sequence of entity 4 (H), FASTA

>6YY0_4 ATP synthase subunit delta, mitochondrial (chains H)
AEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRP
GLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAVTLDMLDLGAAKANLEKAQSELL
GAADEATRAEIQIRIEANEALVKALE

Sequence of entity 5 (I), FASTA

>6YY0_5 ATP synthase subunit epsilon, mitochondrial (chains I)
VAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE

Sequence of entity 6 (J), FASTA

>6YY0_6 ATPase inhibitor, mitochondrial (chains J)
GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEI
HHHHHH

Sequence of entity 7 (S), FASTA

>6YY0_7 ATP synthase subunit O, mitochondrial (chains S)
FAKLVRPPVQIYGIEGRYATALYSAASKQNKLEQVEKELLRVGQILKEPKMAASLLNPYV
KRSVKVKSLSDMTAKEKFSPLTSNLINLLAENGRLTNTPAVISAFSTMMSVHRGEVPCTV
TTASALDEATLTELKTVLKSFLSKGQVLKLEVKIDPSIMGGMIVRIGEKYVDMSAKTKIQ
KLSRAMREIL

Sequence of entity 8 (b), FASTA

>6YY0_8 ATP synthase F(0) complex subunit B1, mitochondrial (chains b)
PVPPLPEHGGKVRFGLIPEEFFQFLYPKTGVTGPYVLGTGLILYLLSKEIYVITPETFSA
ISTIGFLVYIVKKYGASVGEFADKLNEQKIAQLEEVKQASIKQIQDAIDMEKSQQALVQK
RHYLFDVQRNNIAMALEVTYRERLHRVYREVKNRLDYHISVQNMMRQKEQEHMINWVEKR
VVQSISAQQEKETIAKCIADLKLLSKKAQAQPVM

Sequence of entity 9 (d), FASTA

>6YY0_9 ATP synthase subunit d, mitochondrial (chains d)
AGRKLALKTIDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKANV
AKAGLVDDFEKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKELEK
MRNIIPFDQMTIEDLNEVFPETKLDKKKYPYWPHRPIETL

Sequence of entity 10 (h), FASTA

>6YY0_10 ATP synthase-coupling factor 6, mitochondrial (chains h)
NKELDPVQKLFVDKIREYRTKRQTSGGPVDAGPEYQQDLDRELFKLKQMYGKADMNTFPN
FTFEDPKFEVVEKPQS

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

Structure of the dimeric ATP synthase from bovine mitochondria. Spikes, T.E., Montgomery, M.G., Walker, J.E. Proc Natl Acad Sci U S A (2020) 117:23519-23526. DOI 10.1073/pnas.2013998117 · 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.
9VPD 2.3 Å, Cryo-EM structure of the IF1 bound bovine ATP synthase monomer: rotary state 1, F1…
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

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