6ZQN: Bovine ATP synthase monomer state 3

bovine ATP synthase monomer state 3 (combined). Determined by electron microscopy at 4.0 Å resolution. Released 9 Sept 2020.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Bos taurus
Chains: 29
Atoms: 40,080
Mol. weight: 598.48 kDa
Ligands: ATP, MG, ADP, CDL
Released: 9 Sept 2020

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

Secondary structure: helices and β-sheets

6ZQN contains 253 α-helices and 191 β-strands across 29 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 8: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	2-4	3
α-helix	6-8	3
α-helix	9-17	9
α-helix	18-23	6
α-helix	24-29	6
α-helix	34-37	4

Chain a: 13 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-12	2
α-helix	20-25	6
α-helix	28-30	3
β-strand	36	1	49
α-helix	41-58	18
α-helix	63-66	4
α-helix	69-86	18
α-helix	94-96	3
α-helix	98-118	21
α-helix	122-126	5
α-helix	135-137	3
α-helix	138-181	44
α-helix	186-224	39

Chain A: 21 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	52-55	4	2
β-strand	60-66	7	2
β-strand	71-75	5	2
α-helix	79-81	3
β-strand	87-90	4	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	240-259	20
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	354-358	5
β-strand	365	1	6
β-strand	371-372	2	9
α-helix	381-399	19
α-helix	401-403	3
α-helix	412-428	17
α-helix	438-449	12
α-helix	458-473	16
α-helix	477-485	9
α-helix	491-506	16

Chain b: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
β-strand	12-13	2	50
β-strand	17-18	2	50
α-helix	19-29	11
α-helix	32-47	16
α-helix	55-119	65
α-helix	120-122	3
α-helix	123-184	62
α-helix	190-208	19

Chain B: 25 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	185-187	3
β-strand	199-206	8	14
α-helix	210-221	12
β-strand	229-234	6	14
α-helix	240-258	19
β-strand	263-269	7	14
α-helix	271-284	14
α-helix	291-293	3
α-helix	300-306	7
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	458-460	3
α-helix	461-475	15
α-helix	477-486	10
α-helix	491-506	16

Chain C: 21 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	28-35	8	10
β-strand	38-42	5	10
α-helix	47	1
β-strand	48	1	19
β-strand	51-54	4	10
α-helix	55	1
β-strand	60	1	10
β-strand	63-66	4	10
β-strand	70-74	5	10
α-helix	79-81	3
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
α-helix	132-134	3
β-strand	139	1	22
β-strand	145	1	23
α-helix	151-155	5
β-strand	160	1	23
β-strand	164	1	24
β-strand	167-169	3	21
α-helix	175-185	11
α-helix	187-190	4
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	326-328	3	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	461-474	14
α-helix	477-486	10
α-helix	491-505	15

Chain d: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
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
β-strand	131	1	49
α-helix	132-138	7
α-helix	140-142	3

Chain D: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	10
β-strand	20-24	5	10
α-helix	28-31	4
β-strand	34-38	5	10
β-strand	45-51	7	10
β-strand	52	1	3
β-strand	57-62	6	10
β-strand	70	1	19
β-strand	74-81	8	10
β-strand	83-86	4	27
β-strand	95	1	28
β-strand	101	1	28
β-strand	112-115	4	27
α-helix	120-122	3
α-helix	123-125	3
β-strand	126	1	29
β-strand	132-133	2	30
α-helix	138-143	6
α-helix	145	1
β-strand	146-147	2	30
β-strand	152-154	3	31
α-helix	162-169	8
α-helix	170-174	5
β-strand	181-186	6	31
α-helix	190-203	14
β-strand	215-220	6	31
α-helix	226-228	3
α-helix	232-245	14
β-strand	250-256	7	31
α-helix	260-269	10
α-helix	270-272	3
α-helix	285-293	9
β-strand	299	1	29
β-strand	303-309	7	31
α-helix	313-315	3
α-helix	320-325	6
α-helix	326-328	3
β-strand	331-332	2	31
β-strand	335	1	32
α-helix	337-340	4
β-strand	348	1	32
β-strand	354	1	31
α-helix	360-391	32
α-helix	398-413	16
α-helix	420-423	4
α-helix	434-446	13
α-helix	454-456	3
α-helix	463-476	14

21 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 protein 8	8	protein	66	Bos taurus	P03929
ATP synthase subunit a	a	protein	226	Bos taurus	P00847
ATP synthase subunit d, mitochondrial	d	protein	160	Bos taurus	P13620
ATP synthase subunit f, mitochondrial	f	protein	87	Bos taurus	Q28851

6 more molecules are not listed.

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

>6ZQN_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

>6ZQN_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

>6ZQN_3 ATP synthase subunit gamma, mitochondrial (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Sequence of entity 4 (H), FASTA

>6ZQN_4 ATP synthase subunit delta, mitochondrial (chains H)
AEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRP
GLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAVTLDMLDLGAAKANLEKAQSELL
GAADEATRAEIQIRIEANEALVKALE

Sequence of entity 5 (I), FASTA

>6ZQN_5 ATP synthase subunit epsilon, mitochondrial (chains I)
VAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE

Sequence of entity 6 (J), FASTA

>6ZQN_6 ATPase inhibitor, mitochondrial (chains J)
GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEI
HHHHHH

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

>6ZQN_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

>6ZQN_8 ATP synthase subunit O, mitochondrial (chains S)
FAKLVRPPVQIYGIEGRYATALYSAASKQNKLEQVEKELLRVGQILKEPKMAASLLNPYV
KRSVKVKSLSDMTAKEKFSPLTSNLINLLAENGRLTNTPAVISAFSTMMSVHRGEVPCTV
TTASALDEATLTELKTVLKSFLSKGQVLKLEVKIDPSIMGGMIVRIGEKYVDMSAKTKIQ
KLSRAMREIL

Sequence of entity 9 (8), FASTA

>6ZQN_9 ATP synthase protein 8 (chains 8)
MPQLDTSTWLTMILSMFLTLFIIFQLKVSKHNFYHNPELTPTKMLKQNTPWETKWTKIYL
PLLLPL

Sequence of entity 10 (a), FASTA

>6ZQN_10 ATP synthase subunit a (chains a)
MNENLFTSFITPVILGLPLVTLIVLFPSLLFPTSNRLVSNRFVTLQQWMLQLVSKQMMSI
HNSKGQTWTLMLMSLILFIGSTNLLGLLPHSFTPTTQLSMNLGMAIPLWAGAVITGFRNK
TKASLAHFLPQGTPTPLIPMLVIIETISLFIQPMALAVRLTANITAGHLLIHLIGGATLA
LMSISTTTALITFTILILLTILEFAVAMIQAYVFTLLVSLYLHDNT

Sequence of entity 11 (d), FASTA

>6ZQN_11 ATP synthase subunit d, mitochondrial (chains d)
AGRKLALKTIDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKANV
AKAGLVDDFEKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKELEK
MRNIIPFDQMTIEDLNEVFPETKLDKKKYPYWPHRPIETL

Sequence of entity 12 (f), FASTA

>6ZQN_12 ATP synthase subunit f, mitochondrial (chains f)
ASVVPLKEKKLLEVKLGELPSWILMRDFTPSGIAGAFQRGYYRYYNKYVNVKKGSIAGLS
MVLAAYVFLNYCRSYKELKHERLRKYH

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
CDL	Cardiolipin	C81 H156 O17 P2	3
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	2

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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