4Z1M: ATP synthase subunit alpha, mitochondrial

Bovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of thiophosphate. Determined by X-ray diffraction at 3.3 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Bos taurus
Chains: 10
Atoms: 24,201
Mol. weight: 376.76 kDa
Ligands: ADP, MG, ATP
Released: 6 May 2015

Explore 4Z1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Z1M contains 149 α-helices and 157 β-strands across 10 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
β-strand	28-29	2	1
β-strand	31-34	4	1
β-strand	38-41	4	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	88-94	7	1
β-strand	96-99	4	3
α-helix	101-103	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	1	6
α-helix	151-156	6
β-strand	160	1	6
β-strand	164	1	4
β-strand	166-169	4	7
α-helix	175-185	11
α-helix	187-190	4
β-strand	200-206	7	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	287-288	2
β-strand	289	1	8
α-helix	291-293	3
β-strand	295	1	8
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	381-400	20
α-helix	401-406	6
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	491-505	15

Chain B: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
β-strand	28-34	7	1
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	9
β-strand	51-54	4	1
β-strand	60-66	7	1
β-strand	71-76	6	1
β-strand	87-94	8	1
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
α-helix	131-134	4
β-strand	139	1	12
β-strand	145-146	2	13
α-helix	151-156	6
β-strand	159-160	2	13
β-strand	164	1	11
β-strand	166-169	4	14
α-helix	175-185	11
α-helix	187-191	5
β-strand	200-206	7	11
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	11
α-helix	240-259	20
β-strand	263-269	7	11
α-helix	271-285	15
α-helix	291-293	3
α-helix	298-307	10
β-strand	311	1	11
β-strand	312	1	12
α-helix	314-316	3
β-strand	320-325	6	11
β-strand	326-328	3	14
α-helix	337-343	7
β-strand	348-352	5	14
α-helix	354-359	6
β-strand	365	1	14
β-strand	371-372	2	14
α-helix	381-386	6
α-helix	389-399	11
α-helix	414-427	14
α-helix	435-437	3
α-helix	438-449	12
α-helix	461-474	14
α-helix	477-486	10
α-helix	491-509	19

Chain C: 23 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	1
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	15
β-strand	51-54	4	1
β-strand	60-66	7	1
β-strand	71-75	5	1
β-strand	87-88	2	1
β-strand	94	1	1
β-strand	96-99	4	16
β-strand	107-108	2	17
β-strand	114	1	17
β-strand	125-128	4	16
α-helix	131-134	4
β-strand	139	1	18
β-strand	145	1	19
α-helix	151-156	6
α-helix	158-159	2
β-strand	160	1	19
β-strand	164	1	17
β-strand	165-169	5	20
α-helix	175-185	11
α-helix	187-190	4
β-strand	200-207	8	17
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-235	7	17
α-helix	240-259	20
β-strand	263-269	7	17
α-helix	271-283	13
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-307	10
β-strand	311	1	17
β-strand	312	1	18
β-strand	320-323	4	17
β-strand	326-328	3	20
α-helix	337-345	9
β-strand	348-352	5	20
α-helix	354-359	6
β-strand	365	1	20
β-strand	371	1	20
α-helix	381-399	19
α-helix	415-427	13
α-helix	435-437	3
α-helix	438-449	12
α-helix	458-460	3
α-helix	461-475	15
α-helix	477-486	10
α-helix	491-509	19

Chain D: 24 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	20-25	6	1
α-helix	29-31	3
β-strand	35-38	4	1
β-strand	46-52	7	1
β-strand	57-62	6	1
β-strand	70	1	15
β-strand	74-77	4	1
β-strand	83-85	3	21
α-helix	88-90	3
β-strand	91	1	22
β-strand	95	1	23
β-strand	101	1	23
β-strand	113-115	3	21
α-helix	119-122	4
α-helix	123-125	3
β-strand	126	1	24
β-strand	131-132	2	25
α-helix	138-143	6
α-helix	145-146	2
β-strand	147-148	2	25
β-strand	151-156	6	22
α-helix	163-176	14
β-strand	180-185	6	22
α-helix	190-203	14
β-strand	215-219	5	22
α-helix	226-245	20
β-strand	250-256	7	22
α-helix	259-266	8
α-helix	269-272	4
α-helix	278-280	3
α-helix	286-293	8
β-strand	299	1	24
β-strand	303-311	9	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	26
α-helix	337-342	6
β-strand	348	1	26
β-strand	355	1	22
α-helix	365-390	26
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	463-476	14

Chain E: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	20-24	5	1
α-helix	30-31	2
β-strand	35-38	4	1
β-strand	46-54	9	1
β-strand	57-62	6	1
β-strand	70	1	2
β-strand	74-77	4	1
β-strand	83-86	4	27
α-helix	88-90	3
β-strand	94-95	2	28
β-strand	101	1	28
β-strand	112-115	4	27
α-helix	119-122	4
β-strand	132-133	2	29
α-helix	138-143	6
α-helix	145	1
β-strand	146-147	2	29
β-strand	151-155	5	28
α-helix	162-176	15
β-strand	181-186	6	28
α-helix	190-203	14
β-strand	215-220	6	28
α-helix	226-230	5
α-helix	232-245	14
β-strand	250-256	7	28
α-helix	258-271	14
α-helix	278-280	3
α-helix	285-293	9
β-strand	298	1	28
β-strand	303-309	7	28
α-helix	313-315	3
α-helix	320-326	7
β-strand	331-334	4	28
β-strand	335	1	30
α-helix	337-341	5
β-strand	348	1	30
β-strand	355	1	28
α-helix	365-390	26
α-helix	393-395	3
α-helix	398-413	16
α-helix	420-422	3
α-helix	434-446	13
α-helix	463-474	12

Chain F: 24 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	20-25	6	1
β-strand	35-38	4	1
β-strand	46-52	7	1
β-strand	57-62	6	1
α-helix	69	1
β-strand	70	1	9
β-strand	74-77	4	1
β-strand	83-85	3	31
α-helix	88-90	3
β-strand	94-95	2	32
β-strand	101	1	32
β-strand	113-115	3	31
α-helix	119-122	4
α-helix	123-125	3
β-strand	126	1	33
β-strand	131-133	3	34
α-helix	138-143	6
β-strand	146-148	3	34
β-strand	151-156	6	32
α-helix	163-169	7
α-helix	170-174	5
β-strand	181-186	6	32
α-helix	190-203	14
β-strand	215-220	6	32
α-helix	226-242	17
α-helix	243-247	5
β-strand	250-251	2	35
β-strand	252-256	5	32
α-helix	259-272	14
α-helix	278-280	3
α-helix	286-293	8
β-strand	299	1	33
β-strand	303-304	2	35
β-strand	306-311	6	32
α-helix	313-315	3
α-helix	320-325	6
α-helix	326-328	3
β-strand	331-335	5	32
α-helix	337-342	6
β-strand	348	1	32
β-strand	355	1	32
α-helix	365-383	19
α-helix	385-390	6
α-helix	398-413	16
α-helix	422-425	4
α-helix	428-429	2
α-helix	434-446	13
α-helix	463-476	14

Chain G: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-41	39
α-helix	81-90	10
α-helix	110-116	7
α-helix	135-136	2
α-helix	138-146	9
β-strand	165-167	3	36
β-strand	170-171	2	36
α-helix	206-270	65

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-18	5
α-helix	21-49	29

2 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)
ATPase inhibitor, mitochondrial	H, I, J	protein	66	Bos taurus	P01096 (AlphaFold model)

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

>4Z1M_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

>4Z1M_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

>4Z1M_3 ATP synthase subunit gamma, mitochondrial (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Sequence of entity 4 (H, I, J), FASTA

>4Z1M_4 ATPase inhibitor, mitochondrial (chains H, I, J)
GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAAEQLAALKKHHENEISHHAKEI
HHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3

Water and common crystallization additives (CL, GOL) 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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