4YXW: ATP synthase subunit alpha, mitochondrial

Bovine heart mitochondrial F1-ATPase inhibited by AMP-PNP and ADP in the presence of thiophosphate. Determined by X-ray diffraction at 3.1 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Bos taurus
Chains: 9
Atoms: 24,827
Mol. weight: 375.04 kDa
Ligands: TS6, MG, ANP
Released: 6 May 2015

Explore 4YXW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YXW contains 157 α-helices and 169 β-strands across 9 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: 25 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	51-54	4	1
β-strand	60-66	7	1
β-strand	71-75	5	1
β-strand	87-93	7	1
β-strand	96-99	4	3
β-strand	107-108	2	4
β-strand	114	1	4
β-strand	125-128	4	3
α-helix	132-134	3
β-strand	139	1	5
β-strand	145-146	2	6
α-helix	151	1
α-helix	152-156	5
β-strand	159-160	2	6
β-strand	164	1	4
β-strand	165-169	5	7
α-helix	175-185	11
α-helix	187-191	5
β-strand	199-206	8	4
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	4
α-helix	240-259	20
β-strand	263-269	7	4
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-307	10
β-strand	311	1	4
β-strand	312	1	5
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	375-378	4
α-helix	381-400	20
α-helix	401-403	3
α-helix	412-428	17
α-helix	435-437	3
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-474	14
α-helix	477-486	10
α-helix	491-508	18

Chain B: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	28-35	8	1
β-strand	38-43	6	1
α-helix	47-48	2
β-strand	51-55	5	1
β-strand	60-66	7	1
β-strand	71-76	6	1
β-strand	87-94	8	1
β-strand	96-98	3	8
α-helix	101-103	3
β-strand	107-108	2	9
β-strand	114	1	9
β-strand	126-128	3	8
α-helix	131-134	4
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	166-169	4	12
α-helix	175-185	11
α-helix	187-190	4
β-strand	200-206	7	9
α-helix	210-222	13
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	298-307	10
β-strand	311	1	9
β-strand	312	1	10
β-strand	320-323	4	9
β-strand	326-328	3	12
α-helix	337-343	7
β-strand	348-352	5	12
α-helix	354-359	6
β-strand	365	1	12
β-strand	371-372	2	12
α-helix	376-378	3
α-helix	381-395	15
α-helix	412-427	16
α-helix	435-437	3
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-474	14
α-helix	477-486	10
α-helix	491-507	17

Chain C: 26 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	29-34	6	1
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	13
β-strand	51-55	5	1
β-strand	60-66	7	1
β-strand	71-76	6	1
β-strand	87-94	8	1
β-strand	96-98	3	14
α-helix	101-103	3
β-strand	107-108	2	15
β-strand	114	1	15
β-strand	126-128	3	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	18
β-strand	166-169	4	19
α-helix	175-184	10
α-helix	187-190	4
β-strand	200	1	18
β-strand	201-206	6	15
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	15
α-helix	240-259	20
β-strand	263-266	4	18
β-strand	267-269	3	15
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-307	10
β-strand	311	1	18
β-strand	312	1	16
α-helix	314-316	3
β-strand	320-323	4	18
β-strand	326-328	3	19
α-helix	337-345	9
β-strand	348-351	4	19
β-strand	352	1	20
α-helix	354-358	5
β-strand	365	1	20
β-strand	371-372	2	19
α-helix	375-378	4
α-helix	381-386	6
α-helix	390-403	14
α-helix	412-428	17
α-helix	435-437	3
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-474	14
α-helix	477-486	10
α-helix	491-509	19

Chain D: 22 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
β-strand	20-24	5	1
β-strand	35-38	4	1
β-strand	46-52	7	1
β-strand	57-62	6	1
β-strand	70	1	13
β-strand	74-77	4	1
β-strand	83-85	3	21
β-strand	94-95	2	22
β-strand	101	1	22
β-strand	113-115	3	21
α-helix	119-122	4
β-strand	126	1	23
β-strand	132-133	2	24
α-helix	138-143	6
β-strand	146-147	2	24
β-strand	151-156	6	22
α-helix	162-169	8
α-helix	170-174	5
β-strand	181-186	6	22
α-helix	190-203	14
β-strand	215-220	6	22
α-helix	226-242	17
α-helix	243-247	5
β-strand	251-255	5	22
α-helix	259-269	11
α-helix	278-280	3
α-helix	286-293	8
β-strand	299	1	23
β-strand	304-311	8	22
α-helix	313-315	3
α-helix	320-325	6
α-helix	326-328	3
β-strand	331-334	4	22
β-strand	335	1	25
α-helix	337-340	4
β-strand	348	1	25
β-strand	354-355	2	22
α-helix	360-363	4
α-helix	365-388	24
α-helix	393-395	3
α-helix	398-413	16
α-helix	422-425	4
α-helix	434-446	13
α-helix	455-457	3
α-helix	463-472	10

Chain E: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
β-strand	20-24	5	1
β-strand	35-38	4	1
β-strand	46-52	7	1
β-strand	57-62	6	1
β-strand	70	1	2
β-strand	74-77	4	1
β-strand	83-86	4	26
α-helix	88-90	3
β-strand	91	1	27
β-strand	94-95	2	27
β-strand	101	1	27
β-strand	112-115	4	26
α-helix	119-122	4
β-strand	132-133	2	28
α-helix	138-143	6
α-helix	145	1
β-strand	146-147	2	28
β-strand	151-155	5	27
α-helix	162-176	15
β-strand	181-188	8	27
α-helix	190-203	14
β-strand	215-221	7	27
α-helix	226-245	20
β-strand	250-256	7	27
α-helix	258-271	14
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	303-309	7	27
α-helix	313-315	3
α-helix	320-326	7
β-strand	331-334	4	27
β-strand	335	1	29
α-helix	337-340	4
β-strand	348	1	29
β-strand	355	1	27
α-helix	365-384	20
α-helix	398-413	16
α-helix	428-429	2
α-helix	431-433	3
α-helix	434-446	13
α-helix	455-457	3
α-helix	463-472	10

Chain F: 28 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	35-38	4	1
β-strand	46-54	9	1
β-strand	57-62	6	1
β-strand	74-77	4	1
β-strand	83-86	4	30
α-helix	88-90	3
β-strand	94-95	2	31
β-strand	101	1	31
β-strand	112-115	4	30
α-helix	119-122	4
α-helix	123-125	3
β-strand	126	1	32
β-strand	131-133	3	33
α-helix	138-143	6
β-strand	146-148	3	33
β-strand	151-156	6	31
α-helix	162-169	8
α-helix	170-174	5
α-helix	175-176	2
β-strand	180-186	7	31
α-helix	190-203	14
β-strand	215-220	6	31
α-helix	226-241	16
α-helix	242-246	5
β-strand	251-256	6	31
α-helix	259-272	14
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	299	1	32
β-strand	304-311	8	31
α-helix	313-315	3
α-helix	320-325	6
α-helix	326-328	3
β-strand	331-334	4	31
β-strand	335	1	34
α-helix	337-341	5
β-strand	348	1	34
β-strand	354-355	2	31
α-helix	360-363	4
α-helix	365-383	19
α-helix	385-390	6
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	463-473	11

Chain G: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-36	34
α-helix	38-48	11
β-strand	69-70	2	35
β-strand	71	1	36
β-strand	78	1	37
β-strand	80	1	37
α-helix	81-95	15
β-strand	108	1	36
α-helix	110-115	6
β-strand	127-129	3	36
α-helix	135-136	2
α-helix	138-146	9
β-strand	160-161	2	35
β-strand	164-165	2	38
β-strand	171-172	2	38
α-helix	198-269	72

Chain H: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	39
β-strand	26-32	7	39
β-strand	35-37	3	40
β-strand	46-48	3	40
β-strand	61-66	6	40
β-strand	72-77	6	40
β-strand	80-81	2	39
β-strand	89-94	6	39
β-strand	97-99	3	40
α-helix	100-102	3
α-helix	105-119	15
α-helix	125-144	20

1 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

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

>4YXW_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

>4YXW_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

>4YXW_3 ATP synthase subunit gamma, mitochondrial (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Sequence of entity 4 (H), FASTA

>4YXW_4 ATP synthase subunit delta, mitochondrial (chains H)
AEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRP
GLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAVTLDMLDLGAAKANLEKAQSELL
GAADEATRAEIQIRIEANEALVKALE

Sequence of entity 5 (I), FASTA

>4YXW_5 ATP synthase subunit epsilon, mitochondrial (chains I)
VAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE

Ligands and cofactors

ID	Name	Formula	Copies
TS6	Monothiophosphate	H3 O3 P S	1
MG	Magnesium ion	Mg	5
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	5

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

How release of phosphate from mammalian F1-ATPase generates a rotary substep. Bason, J.V., Montgomery, M.G., Leslie, A.G. et al. Proc Natl Acad Sci U S A (2015) 112:6009-6014. DOI 10.1073/pnas.1506465112 · 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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