6Z1U: ATP synthase subunit alpha, mitochondrial

bovine ATP synthase F1c8-peripheral stalk domain, state 3. Determined by electron microscopy at 3.47 Å resolution. Released 9 Sept 2020.

Method: Electron microscopy
Resolution: 3.47 Å
Organism: Bos taurus
Chains: 21
Atoms: 32,270
Mol. weight: 498.46 kDa
Ligands: ATP, MG, ADP
Released: 9 Sept 2020

Explore 6Z1U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z1U contains 197 α-helices and 185 β-strands across 21 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: 23 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
β-strand	26	1	1
β-strand	29-33	5	2
β-strand	34	1	3
β-strand	38-43	6	2
α-helix	47	1
β-strand	48	1	4
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	96-98	3	5
β-strand	107-109	3	6
β-strand	114	1	6
β-strand	126-128	3	5
α-helix	131-134	4
β-strand	139	1	7
β-strand	145	1	8
α-helix	151-155	5
β-strand	160	1	8
β-strand	164	1	6
β-strand	166	1	9
β-strand	167-169	3	6
α-helix	175-185	11
α-helix	187-191	5
β-strand	199-206	8	6
α-helix	210-222	13
β-strand	230-234	5	6
α-helix	240-244	5
α-helix	246-259	14
β-strand	263-269	7	6
α-helix	274-285	12
α-helix	291-293	3
α-helix	300-306	7
β-strand	312	1	7
β-strand	320-323	4	6
β-strand	326-328	3	6
α-helix	337-343	7
β-strand	348-349	2	9
β-strand	352	1	6
α-helix	354-359	6
β-strand	365	1	6
β-strand	371-372	2	9
α-helix	381-399	19
α-helix	401-405	5
α-helix	412-428	17
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-473	13
α-helix	477-485	9
α-helix	491-506	16

Chain b: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	164-184	21
α-helix	190-207	18

Chain B: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
α-helix	19-21	3
β-strand	28-35	8	10
β-strand	38-43	6	10
α-helix	47	1
β-strand	48	1	11
β-strand	51	1	12
β-strand	52-54	3	10
β-strand	60-66	7	10
β-strand	71-75	5	10
α-helix	79-81	3
β-strand	87-89	3	10
β-strand	94	1	12
β-strand	96-99	4	13
β-strand	107-109	3	14
β-strand	114	1	14
β-strand	125-128	4	13
α-helix	131-134	4
β-strand	139	1	15
β-strand	145	1	16
α-helix	151-156	6
β-strand	160	1	16
β-strand	164	1	14
β-strand	167-168	2	17
α-helix	175-184	10
α-helix	189-191	3
β-strand	199-206	8	14
α-helix	210-222	13
β-strand	229-234	6	14
α-helix	240-258	19
β-strand	263-269	7	14
α-helix	271-283	13
α-helix	303-306	4
β-strand	312	1	15
β-strand	320-323	4	14
β-strand	326-327	2	17
α-helix	337-343	7
β-strand	348	1	18
β-strand	350-352	3	17
α-helix	354-358	5
β-strand	365-366	2	17
β-strand	372	1	18
α-helix	375-377	3
α-helix	381-399	19
α-helix	400-402	3
α-helix	412-428	17
α-helix	438-449	12
α-helix	452-455	4
α-helix	458-475	18
α-helix	477-486	10
α-helix	491-506	16

Chain C: 17 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	28-35	8	10
β-strand	38-42	5	10
β-strand	48	1	19
β-strand	51-55	5	10
β-strand	60-66	7	10
β-strand	70-75	6	10
β-strand	87-94	8	10
β-strand	96-98	3	20
α-helix	101-103	3
β-strand	106-109	4	21
β-strand	114	1	21
β-strand	126-128	3	20
β-strand	139	1	22
β-strand	145	1	23
α-helix	151-154	4
β-strand	160	1	23
β-strand	164	1	24
β-strand	167-169	3	21
α-helix	176-185	10
β-strand	199	1	25
β-strand	201-206	6	21
α-helix	210-221	12
β-strand	229-234	6	21
α-helix	240-259	20
β-strand	263	1	25
β-strand	265-266	2	24
β-strand	267-269	3	21
α-helix	272-283	12
α-helix	291-293	3
α-helix	298-306	9
β-strand	312	1	22
β-strand	322-323	2	24
β-strand	326-327	2	21
α-helix	337-343	7
β-strand	348	1	26
β-strand	351-352	2	21
β-strand	365-366	2	21
β-strand	372	1	26
α-helix	375-378	4
α-helix	381-399	19
α-helix	412-428	17
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-474	14
α-helix	477-486	10
α-helix	491-505	15

Chain D: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	10
β-strand	24-28	5	10
α-helix	32-35	4
β-strand	38-42	5	10
β-strand	49-55	7	10
β-strand	56	1	3
β-strand	61-66	6	10
β-strand	74	1	19
β-strand	78-85	8	10
β-strand	87-90	4	27
β-strand	99	1	28
β-strand	105	1	28
β-strand	116-119	4	27
α-helix	124-126	3
α-helix	127-129	3
β-strand	130	1	29
β-strand	136-137	2	30
α-helix	142-147	6
α-helix	149	1
β-strand	150-151	2	30
β-strand	156-158	3	31
α-helix	166-173	8
α-helix	174-178	5
β-strand	185-190	6	31
α-helix	195-207	13
β-strand	219-224	6	31
α-helix	230-232	3
α-helix	236-249	14
β-strand	254-260	7	31
α-helix	264-273	10
α-helix	274-276	3
α-helix	289-297	9
β-strand	303	1	29
β-strand	307-313	7	31
α-helix	317-319	3
α-helix	324-329	6
α-helix	330-332	3
β-strand	335-336	2	31
β-strand	339	1	32
α-helix	341-344	4
β-strand	352	1	32
β-strand	358	1	31
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

Chain E: 24 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	2
β-strand	24-28	5	2
α-helix	33-35	3
β-strand	38-42	5	2
β-strand	50-56	7	2
β-strand	61-66	6	2
β-strand	74	1	4
β-strand	78-85	8	2
β-strand	87-89	3	33
α-helix	92-94	3
β-strand	98-99	2	34
β-strand	105	1	34
β-strand	117-119	3	33
α-helix	123-126	4
β-strand	137	1	35
α-helix	142-147	6
α-helix	149	1
β-strand	150	1	35
α-helix	151	1
β-strand	155-158	4	34
α-helix	167-180	14
β-strand	187-192	6	34
α-helix	194-207	14
β-strand	221-225	5	34
α-helix	230-232	3
α-helix	237-251	15
β-strand	254-255	2	36
β-strand	258-259	2	34
α-helix	263-275	13
α-helix	278-280	3
α-helix	289-297	9
β-strand	307-308	2	36
β-strand	310-313	4	34
α-helix	317-319	3
α-helix	324-329	6
β-strand	333	1	34
β-strand	335	1	37
β-strand	339	1	38
α-helix	342-345	4
β-strand	352	1	38
β-strand	359	1	37
α-helix	369-394	26
α-helix	397-399	3
α-helix	402-418	17
α-helix	426-429	4
α-helix	431-433	3
α-helix	438-449	12
α-helix	458-460	3
α-helix	467-477	11

Chain F: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	10
β-strand	24-29	6	10
α-helix	32-35	4
β-strand	39-43	5	10
β-strand	50-58	9	10
β-strand	61-66	6	10
β-strand	74	1	11
β-strand	78-81	4	10
β-strand	87-90	4	39
β-strand	98-99	2	40
β-strand	105	1	40
β-strand	116-119	4	39
α-helix	122-126	5
α-helix	127-129	3
β-strand	130	1	41
β-strand	136-137	2	42
α-helix	142-146	5
β-strand	150-151	2	42
β-strand	156-159	4	40
α-helix	166-178	13
β-strand	186-190	5	40
α-helix	194-205	12
β-strand	220-224	5	40
α-helix	230-233	4
α-helix	236-249	14
β-strand	255-259	5	40
α-helix	264-271	8
α-helix	278-280	3
α-helix	289-297	9
β-strand	303	1	41
β-strand	308-312	5	40
α-helix	317-319	3
α-helix	324-329	6
α-helix	330-332	3
β-strand	335-338	4	40
β-strand	339	1	43
α-helix	341-344	4
β-strand	352	1	43
β-strand	358-359	2	40
α-helix	364-394	31
α-helix	397-399	3
α-helix	402-418	17
α-helix	423-425	3
α-helix	431-433	3
α-helix	438-449	12
α-helix	458-460	3
α-helix	467-478	12

Chain G: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-54	52
β-strand	66-71	6	44
α-helix	80-98	19
β-strand	103-108	6	44
α-helix	110-120	11
β-strand	124-129	6	44
α-helix	138-149	12
β-strand	157-167	11	44
β-strand	170-179	10	44
α-helix	181-184	4
β-strand	194	1	45
α-helix	200-270	71

12 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 F(0) complex subunit C2, mitochondrial	K, L, M, N, O, P, Q, R	protein	75	Bos taurus	P07926
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-coupling factor 6, mitochondrial	h	protein	76	Bos taurus	P02721

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

>6Z1U_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

>6Z1U_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

>6Z1U_3 ATP synthase subunit gamma, mitochondrial (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Sequence of entity 4 (H), FASTA

>6Z1U_4 ATP synthase subunit delta, mitochondrial (chains H)
AEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRP
GLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAVTLDMLDLGAAKANLEKAQSELL
GAADEATRAEIQIRIEANEALVKALE

Sequence of entity 5 (I), FASTA

>6Z1U_5 ATP synthase subunit epsilon, mitochondrial (chains I)
VAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE

Sequence of entity 6 (J), FASTA

>6Z1U_6 ATPase inhibitor, mitochondrial (chains J)
GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEI
HHHHHH

Sequence of entity 7 (K, L, M, N, O, P, Q, R), FASTA

>6Z1U_7 ATP synthase F(0) complex subunit C2, mitochondrial (chains K, L, M, N, O, P, Q, R)
DIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAM
GLFCLMVAFLILFAM

Sequence of entity 8 (S), FASTA

>6Z1U_8 ATP synthase subunit O, mitochondrial (chains S)
FAKLVRPPVQIYGIEGRYATALYSAASKQNKLEQVEKELLRVGQILKEPKMAASLLNPYV
KRSVKVKSLSDMTAKEKFSPLTSNLINLLAENGRLTNTPAVISAFSTMMSVHRGEVPCTV
TTASALDEATLTELKTVLKSFLSKGQVLKLEVKIDPSIMGGMIVRIGEKYVDMSAKTKIQ
KLSRAMREIL

Sequence of entity 9 (b), FASTA

>6Z1U_9 ATP synthase F(0) complex subunit B1, mitochondrial (chains b)
PVPPLPEHGGKVRFGLIPEEFFQFLYPKTGVTGPYVLGTGLILYLLSKEIYVITPETFSA
ISTIGFLVYIVKKYGASVGEFADKLNEQKIAQLEEVKQASIKQIQDAIDMEKSQQALVQK
RHYLFDVQRNNIAMALEVTYRERLHRVYREVKNRLDYHISVQNMMRQKEQEHMINWVEKR
VVQSISAQQEKETIAKCIADLKLLSKKAQAQPVM

Sequence of entity 10 (h), FASTA

>6Z1U_10 ATP synthase-coupling factor 6, mitochondrial (chains h)
NKELDPVQKLFVDKIREYRTKRQTSGGPVDAGPEYQQDLDRELFKLKQMYGKADMNTFPN
FTFEDPKFEVVEKPQS

Ligands and cofactors

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