2XND: Bovine F1-c8 sub-complex of ATP Synthase

Crystal structure of bovine F1-c8 sub-complex of ATP Synthase. Determined by X-ray diffraction at 3.5 Å resolution. Released 15 Sept 2010.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: BOS TAURUS
Chains: 17
Atoms: 28,196
Mol. weight: 421.72 kDa
Ligands: MG, ANP
Released: 15 Sept 2010

Explore 2XND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XND contains 208 α-helices and 173 β-strands across 17 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: 26 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	28-35	8	1
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	2
β-strand	52-54	3	1
β-strand	60-66	7	1
β-strand	71-76	6	1
β-strand	87-90	4	1
β-strand	96-98	3	3
α-helix	101-103	3
β-strand	107-109	3	4
β-strand	114	1	4
β-strand	126-128	3	3
α-helix	131-134	4
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	165-169	5	7
α-helix	175-185	11
α-helix	187-191	5
β-strand	200-208	9	4
α-helix	210-221	12
α-helix	226-228	3
β-strand	229-235	7	4
α-helix	240-259	20
β-strand	263-269	7	4
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	296-298	3
α-helix	299-306	8
β-strand	311	1	4
β-strand	312	1	5
α-helix	314-316	3
β-strand	320-325	6	4
β-strand	326-328	3	7
α-helix	337-345	9
β-strand	348-352	5	7
α-helix	354-359	6
β-strand	365	1	7
β-strand	371-372	2	7
α-helix	375-377	3
α-helix	381-398	18
α-helix	401-403	3
α-helix	412-428	17
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-475	15
α-helix	477-486	10
α-helix	491-508	18

Chain B: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	1
β-strand	33-35	3	1
β-strand	38-41	4	1
β-strand	51-54	4	1
β-strand	60-66	7	1
β-strand	71-75	5	1
α-helix	79-81	3
α-helix	86-88	3
β-strand	89-94	6	1
β-strand	96-99	4	8
β-strand	107-108	2	9
β-strand	114	1	9
β-strand	125-128	4	8
α-helix	131-133	3
β-strand	139	1	10
β-strand	145	1	11
α-helix	151-156	6
β-strand	160	1	11
β-strand	164	1	9
β-strand	166-170	5	12
α-helix	175-185	11
α-helix	187-190	4
β-strand	200-206	7	9
α-helix	210-221	12
α-helix	226-228	3
β-strand	229-234	6	9
α-helix	240-258	19
β-strand	263-269	7	9
α-helix	271-284	14
α-helix	291-293	3
α-helix	298-306	9
β-strand	311	1	9
β-strand	312	1	10
α-helix	314-316	3
β-strand	320-325	6	9
β-strand	326-329	4	12
α-helix	337-343	7
β-strand	348-352	5	12
α-helix	354-357	4
β-strand	365	1	12
β-strand	371-372	2	12
α-helix	373-378	6
α-helix	381-397	17
α-helix	415-426	12
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-474	14
α-helix	477-484	8
α-helix	491-507	17

Chain C: 28 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	28-35	8	1
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	13
β-strand	51-55	5	1
β-strand	60-65	6	1
β-strand	66	1	14
β-strand	71-75	5	1
β-strand	87-94	8	1
β-strand	96-99	4	15
α-helix	101-103	3
β-strand	107-109	3	16
β-strand	114	1	16
β-strand	125-128	4	15
α-helix	132-134	3
β-strand	139	1	17
β-strand	145	1	18
α-helix	151-156	6
β-strand	160	1	18
β-strand	164	1	16
β-strand	166-169	4	19
α-helix	175-184	10
α-helix	187-190	4
β-strand	199-206	8	16
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	16
α-helix	240-259	20
β-strand	263-269	7	16
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-308	11
β-strand	311	1	16
β-strand	312	1	17
α-helix	314-316	3
β-strand	320-325	6	16
β-strand	326-328	3	19
α-helix	329	1
α-helix	337-343	7
β-strand	348-352	5	19
α-helix	354-359	6
β-strand	365	1	19
β-strand	371-372	2	19
α-helix	375-378	4
α-helix	381-387	7
α-helix	390-403	14
α-helix	404-406	3
α-helix	412-427	16
α-helix	435-437	3
α-helix	438-450	13
α-helix	458-460	3
α-helix	461-475	15
α-helix	477-486	10
α-helix	491-506	16

Chain D: 27 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	14
β-strand	20-25	6	14
α-helix	29-30	2
β-strand	34-38	5	14
β-strand	46-54	9	14
β-strand	57-62	6	14
α-helix	69	1
β-strand	70	1	13
β-strand	74-81	8	14
β-strand	83-86	4	20
α-helix	88-90	3
β-strand	94-95	2	21
β-strand	101	1	21
β-strand	112-115	4	20
α-helix	119-122	4
α-helix	123-125	3
β-strand	126	1	22
β-strand	132-133	2	23
α-helix	138-143	6
α-helix	145	1
β-strand	146-147	2	23
β-strand	151-156	6	21
α-helix	162-169	8
α-helix	170-174	5
β-strand	180-186	7	21
α-helix	190-203	14
β-strand	215-220	6	21
α-helix	226-229	4
α-helix	232-245	14
β-strand	251-256	6	21
α-helix	259-272	14
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	299	1	22
β-strand	302	1	22
β-strand	304-311	8	21
α-helix	313-315	3
α-helix	320-325	6
α-helix	326-328	3
β-strand	331-334	4	21
β-strand	335	1	24
α-helix	337-341	5
β-strand	348	1	24
β-strand	354-355	2	21
α-helix	360-363	4
α-helix	365-390	26
α-helix	401-413	13
α-helix	422-425	4
α-helix	434-446	13
α-helix	454-456	3
α-helix	463-474	12

Chain E: 23 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
β-strand	20-25	6	1
α-helix	29-31	3
β-strand	34-38	5	1
β-strand	46-54	9	1
β-strand	57-62	6	1
β-strand	70	1	2
β-strand	74-81	8	1
β-strand	83-86	4	25
α-helix	88-90	3
β-strand	94-95	2	26
β-strand	101	1	26
β-strand	112-115	4	25
α-helix	119-122	4
β-strand	132	1	27
α-helix	138-143	6
α-helix	145-146	2
β-strand	147	1	27
β-strand	151-155	5	26
α-helix	162-176	15
β-strand	181-188	8	26
α-helix	190-201	12
β-strand	215-221	7	26
α-helix	226-245	20
β-strand	250-256	7	26
α-helix	259-272	14
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	298	1	26
β-strand	303-310	8	26
α-helix	313-315	3
α-helix	320-326	7
β-strand	331-334	4	26
β-strand	335	1	28
α-helix	337-342	6
β-strand	348	1	28
β-strand	355	1	26
α-helix	365-383	19
α-helix	385-389	5
α-helix	393-395	3
α-helix	398-413	16
α-helix	428-429	2
α-helix	434-445	12
α-helix	454-456	3
α-helix	464-471	8

Chain F: 25 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
β-strand	20-24	5	1
β-strand	34-38	5	1
β-strand	46-52	7	1
β-strand	57-62	6	1
β-strand	74-81	8	1
β-strand	83-85	3	29
α-helix	88-90	3
β-strand	91	1	30
β-strand	94-95	2	30
β-strand	101	1	30
β-strand	113-115	3	29
α-helix	123-125	3
β-strand	126	1	31
β-strand	132	1	32
α-helix	138-143	6
β-strand	147	1	32
β-strand	151-156	6	30
α-helix	162-169	8
α-helix	170-174	5
β-strand	181-186	6	30
α-helix	191-203	13
β-strand	215-220	6	30
α-helix	226-245	20
β-strand	250-256	7	30
α-helix	259-272	14
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	299	1	31
β-strand	303-311	9	30
α-helix	312	1
α-helix	313-315	3
α-helix	320-325	6
α-helix	326-328	3
β-strand	331-334	4	30
β-strand	335	1	33
α-helix	337-341	5
β-strand	348	1	33
β-strand	354-355	2	30
α-helix	360-363	4
α-helix	365-391	27
α-helix	393-395	3
α-helix	398-413	16
α-helix	422-425	4
α-helix	428-429	2
α-helix	434-446	13
α-helix	454-457	4
α-helix	464-472	9

Chain G: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-36	34
α-helix	38-49	12
β-strand	68-71	4	34
α-helix	82-95	14
β-strand	105-108	4	34
α-helix	110-113	4
β-strand	124-128	5	34
β-strand	131	1	35
β-strand	134	1	35
α-helix	138-150	13
β-strand	158-165	8	34
β-strand	171-178	8	34
α-helix	190-192	3
α-helix	198-269	72

Chain H: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	36
β-strand	26-32	7	36
β-strand	35-38	4	37
β-strand	40	1	38
β-strand	45-47	3	37
β-strand	56-57	2	36
β-strand	58	1	38
β-strand	61-66	6	37
α-helix	71-72	2
β-strand	73-77	5	37
β-strand	80-84	5	36
β-strand	89-94	6	36
β-strand	97-99	3	37
α-helix	100-102	3
β-strand	103	1	39
α-helix	107-118	12
α-helix	125-139	15

9 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	492	BOS TAURUS	P19483 (AlphaFold model)
ATP synthase subunit beta, mitochondrial	D, E, F	protein	467	BOS TAURUS	P00829 (AlphaFold model)
ATP synthase subunit gamma, mitochondrial	G	protein	272	BOS TAURUS	P05631 (AlphaFold model)
ATP synthase subunit delta, mitochondrial	H	protein	131	BOS TAURUS	P05630 (AlphaFold model)
ATP synthase subunit epsilon, mitochondrial	I	protein	47	BOS TAURUS	P05632
ATP synthase lipid-binding protein, mitochondrial	J, K, L, M, N, O, P, Q	protein	72	BOS TAURUS	P32876

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

>2XND_1 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL (chains A, B, C)
ADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGN
DKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIP
RISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKK
LYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFR
DNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGG
GSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAI
EEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLK
EIVTNFLAGFEA

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

>2XND_2 ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL (chains D, E, F)
TTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEG
LVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSV
EQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGE
RTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEG
QDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQ
AIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHY
DVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHL
GKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAE

Sequence of entity 3 (G), FASTA

>2XND_3 ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAAL

Sequence of entity 4 (H), FASTA

>2XND_4 ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL (chains H)
QMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK
YFVSSGSVTVNADSSVQLLAEEAVTLDMLDLGAAKANLEKAQSELLGAADEATRAEIQIR
IEANEALVKAL

Sequence of entity 5 (I), FASTA

>2XND_5 ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL (chains I)
VAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKV

Sequence of entity 6 (J, K, L, M, N, O, P, Q), FASTA

>2XND_6 ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL (chains J, K, L, M, N, O, P, Q)
IDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMG
LFCLMVAFLILF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	5

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Bioenergetic Cost of Making an Adenosine Triphosphate Molecule in Animal Mitochondria. Watt, I.N., Montgomery, M.G., Runswick, M.J. et al. Proc Natl Acad Sci U S A (2010) 107:16823. DOI 10.1073/PNAS.1011099107 · 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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