6ZQM: Bovine ATP synthase monomer state 2

bovine ATP synthase monomer state 2 (combined). Determined by electron microscopy at 3.29 Å resolution. Released 9 Sept 2020.

Method: Electron microscopy
Resolution: 3.29 Å
Organism: Bos taurus
Chains: 29
Atoms: 40,002
Mol. weight: 598.48 kDa
Ligands: LHG, CDL, ADP, MG
Released: 9 Sept 2020

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

Secondary structure: helices and β-sheets

6ZQM contains 253 α-helices and 187 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: 5 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	24-28	5

Chain a: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-12	2
α-helix	20-29	10
β-strand	36	1	43
α-helix	41-58	18
α-helix	63-85	23
α-helix	94-96	3
α-helix	98-119	22
α-helix	121-126	6
α-helix	135-137	3
α-helix	139-181	43
α-helix	186-224	39

Chain A: 23 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	1
β-strand	34	1	2
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	3
β-strand	51-55	5	1
β-strand	60-66	7	1
β-strand	71-75	5	1
α-helix	79-81	3
β-strand	87-94	8	1
β-strand	96-98	3	4
β-strand	107-109	3	5
β-strand	114	1	5
β-strand	126-128	3	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	1	8
β-strand	167-169	3	5
α-helix	175-185	11
α-helix	187-190	4
β-strand	199-206	8	5
α-helix	210-222	13
β-strand	229-234	6	5
α-helix	240-258	19
β-strand	263-269	7	5
α-helix	272-285	14
α-helix	291-293	3
α-helix	300-306	7
β-strand	311	1	5
β-strand	312	1	6
α-helix	314-316	3
β-strand	320-323	4	5
β-strand	326-328	3	5
α-helix	330-332	3
α-helix	337-343	7
β-strand	348-349	2	8
β-strand	352	1	5
α-helix	354-358	5
β-strand	365	1	5
β-strand	371-372	2	8
α-helix	375-378	4
α-helix	381-398	18
α-helix	402-405	4
α-helix	412-427	16
α-helix	438-450	13
α-helix	458-474	17
α-helix	477-486	10
α-helix	491-506	16

Chain b: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	12-13	2	45
β-strand	17-18	2	45
α-helix	19-29	11
α-helix	32-47	16
α-helix	55-120	66
α-helix	123-184	62
α-helix	190-208	19

Chain B: 25 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
β-strand	26-27	2	9
β-strand	28-35	8	2
β-strand	38-43	6	2
α-helix	47-48	2
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	10
α-helix	101-103	3
β-strand	107-108	2	11
β-strand	114	1	11
β-strand	125-128	4	10
β-strand	139	1	12
β-strand	145	1	13
α-helix	151-155	5
β-strand	160	1	13
β-strand	164	1	11
β-strand	167-169	3	11
α-helix	175-185	11
α-helix	189-191	3
β-strand	200-206	7	11
α-helix	210-222	13
β-strand	230-234	5	11
α-helix	240-243	4
α-helix	246-259	14
β-strand	263-269	7	11
α-helix	275-285	11
α-helix	291-293	3
α-helix	296-298	3
α-helix	300-306	7
β-strand	312	1	12
α-helix	314-316	3
β-strand	320-323	4	11
β-strand	326-328	3	11
α-helix	330-332	3
α-helix	337-343	7
β-strand	348-349	2	14
β-strand	350-352	3	11
α-helix	354-358	5
β-strand	365	1	11
β-strand	371-372	2	14
α-helix	381-400	20
α-helix	412-428	17
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-475	15
α-helix	477-485	9
α-helix	491-506	16

Chain C: 23 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
α-helix	20-22	3
β-strand	28-35	8	2
β-strand	38-43	6	2
α-helix	47	1
β-strand	48	1	15
β-strand	51-54	4	2
β-strand	60-66	7	2
β-strand	71-75	5	2
α-helix	79-81	3
α-helix	86	1
β-strand	87-94	8	2
β-strand	96-99	4	16
β-strand	108	1	17
β-strand	109	1	18
β-strand	114	1	17
β-strand	125-128	4	16
α-helix	132-134	3
β-strand	139	1	19
β-strand	145	1	20
α-helix	151-156	6
β-strand	160	1	20
β-strand	164	1	18
β-strand	167-169	3	18
α-helix	175-185	11
α-helix	187-190	4
β-strand	199-206	8	18
α-helix	210-222	13
β-strand	229-234	6	18
α-helix	240-259	20
β-strand	263-269	7	18
α-helix	271-284	14
α-helix	291-293	3
α-helix	298-306	9
β-strand	312	1	19
α-helix	314-316	3
β-strand	320-323	4	18
β-strand	326-328	3	18
α-helix	337-343	7
β-strand	349	1	21
β-strand	350-352	3	18
β-strand	365	1	18
β-strand	367	1	22
β-strand	370	1	22
β-strand	371	1	21
α-helix	375-378	4
α-helix	381-397	17
α-helix	413-428	16
α-helix	438-450	13
α-helix	458-475	18
α-helix	477-486	10
α-helix	491-506	16

Chain d: 13 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	16-18	3
α-helix	21-23	3
α-helix	24-43	20
α-helix	53-59	7
α-helix	63-75	13
α-helix	87-98	12
α-helix	99-105	7
α-helix	106-122	17
α-helix	124-126	3
α-helix	127-129	3
β-strand	131	1	43
α-helix	132-138	7
α-helix	140-142	3

Chain D: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	2
β-strand	20-25	6	2
α-helix	29-31	3
β-strand	34-38	5	2
β-strand	46-52	7	2
β-strand	57-62	6	2
β-strand	70	1	15
β-strand	74-81	8	2
α-helix	82	1
β-strand	83-86	4	23
β-strand	94-95	2	24
β-strand	101	1	24
β-strand	112-115	4	23
α-helix	119-122	4
α-helix	123-125	3
β-strand	132	1	25
α-helix	138-143	6
β-strand	147	1	25
β-strand	152-156	5	24
α-helix	162-169	8
α-helix	170-174	5
α-helix	175	1
β-strand	182-186	5	24
α-helix	190-203	14
β-strand	216-220	5	24
α-helix	226-229	4
α-helix	232-245	14
β-strand	250-255	6	24
α-helix	260-272	13
α-helix	285-293	9
β-strand	299	1	26
β-strand	302	1	26
β-strand	303-311	9	24
α-helix	313-315	3
α-helix	320-325	6
α-helix	326-328	3
β-strand	331-332	2	24
β-strand	335	1	27
α-helix	337-341	5
β-strand	348	1	27
β-strand	354-355	2	24
α-helix	365-391	27
α-helix	401-414	14
α-helix	419-421	3
α-helix	422-425	4
α-helix	434-446	13
α-helix	454-457	4
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

>6ZQM_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

>6ZQM_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

>6ZQM_3 ATP synthase subunit gamma, mitochondrial (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Sequence of entity 4 (H), FASTA

>6ZQM_4 ATP synthase subunit delta, mitochondrial (chains H)
AEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRP
GLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAVTLDMLDLGAAKANLEKAQSELL
GAADEATRAEIQIRIEANEALVKALE

Sequence of entity 5 (I), FASTA

>6ZQM_5 ATP synthase subunit epsilon, mitochondrial (chains I)
VAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE

Sequence of entity 6 (J), FASTA

>6ZQM_6 ATPase inhibitor, mitochondrial (chains J)
GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEI
HHHHHH

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

>6ZQM_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

>6ZQM_8 ATP synthase subunit O, mitochondrial (chains S)
FAKLVRPPVQIYGIEGRYATALYSAASKQNKLEQVEKELLRVGQILKEPKMAASLLNPYV
KRSVKVKSLSDMTAKEKFSPLTSNLINLLAENGRLTNTPAVISAFSTMMSVHRGEVPCTV
TTASALDEATLTELKTVLKSFLSKGQVLKLEVKIDPSIMGGMIVRIGEKYVDMSAKTKIQ
KLSRAMREIL

Sequence of entity 9 (8), FASTA

>6ZQM_9 ATP synthase protein 8 (chains 8)
MPQLDTSTWLTMILSMFLTLFIIFQLKVSKHNFYHNPELTPTKMLKQNTPWETKWTKIYL
PLLLPL

Sequence of entity 10 (a), FASTA

>6ZQM_10 ATP synthase subunit a (chains a)
MNENLFTSFITPVILGLPLVTLIVLFPSLLFPTSNRLVSNRFVTLQQWMLQLVSKQMMSI
HNSKGQTWTLMLMSLILFIGSTNLLGLLPHSFTPTTQLSMNLGMAIPLWAGAVITGFRNK
TKASLAHFLPQGTPTPLIPMLVIIETISLFIQPMALAVRLTANITAGHLLIHLIGGATLA
LMSISTTTALITFTILILLTILEFAVAMIQAYVFTLLVSLYLHDNT

Sequence of entity 11 (d), FASTA

>6ZQM_11 ATP synthase subunit d, mitochondrial (chains d)
AGRKLALKTIDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKANV
AKAGLVDDFEKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKELEK
MRNIIPFDQMTIEDLNEVFPETKLDKKKYPYWPHRPIETL

Sequence of entity 12 (f), FASTA

>6ZQM_12 ATP synthase subunit f, mitochondrial (chains f)
ASVVPLKEKKLLEVKLGELPSWILMRDFTPSGIAGAFQRGYYRYYNKYVNVKKGSIAGLS
MVLAAYVFLNYCRSYKELKHERLRKYH

Ligands and cofactors

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