1W0J: Beryllium fluoride inhibited bovine F1-ATPase

Beryllium fluoride inhibited bovine F1-ATPase. Determined by X-ray diffraction at 2.2 Å resolution. Released 8 Jul 2004.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: BOS TAURUS
Chains: 7
Atoms: 24,480
Mol. weight: 354.22 kDa
Ligands: PO4, BEF, MG, ADP
Released: 8 Jul 2004

Explore 1W0J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1W0J contains 163 α-helices and 157 β-strands across 7 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, 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	2
β-strand	52-55	4	1
β-strand	60-67	8	1
β-strand	70-76	7	1
α-helix	79-81	3
β-strand	87-89	3	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	145-146	2	6
α-helix	151-156	6
β-strand	159-160	2	6
β-strand	164	1	4
β-strand	165-169	5	7
α-helix	175-185	11
α-helix	187-190	4
α-helix	195-197	3
β-strand	200-206	7	4
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	4
α-helix	240-258	19
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	310-311	2	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	348-351	4	7
β-strand	352	1	8
α-helix	354-358	5
β-strand	365	1	8
β-strand	371-372	2	7
α-helix	375-378	4
α-helix	381-398	18
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	491-508	18

Chain B: 26 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	28-34	7	1
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	9
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	96-99	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	1	13
α-helix	151-156	6
β-strand	160	1	13
β-strand	164	1	11
β-strand	166-169	4	14
α-helix	175-185	11
α-helix	187-190	4
β-strand	200-206	7	11
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	11
α-helix	240-258	19
β-strand	263-269	7	11
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-306	9
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	354-358	5
β-strand	365	1	14
β-strand	371-372	2	14
α-helix	375-378	4
α-helix	381-398	18
α-helix	412-427	16
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	491-507	17

Chain C: 28 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
β-strand	28-35	8	1
β-strand	38-43	6	1
α-helix	47	1
β-strand	48	1	15
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	96-99	4	16
α-helix	101-103	3
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
β-strand	160	1	19
β-strand	164	1	17
β-strand	166-169	4	20
α-helix	175-185	11
α-helix	187-190	4
β-strand	200-206	7	17
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	17
α-helix	240-258	19
β-strand	263-269	7	17
α-helix	271-284	14
α-helix	287-289	3
α-helix	291-293	3
α-helix	298-306	9
β-strand	311	1	17
β-strand	312	1	18
α-helix	314-316	3
β-strand	320-325	6	17
β-strand	326-328	3	20
α-helix	337-343	7
β-strand	348-352	5	20
α-helix	354-359	6
β-strand	365	1	20
β-strand	371-372	2	20
α-helix	375-378	4
α-helix	381-387	7
α-helix	390-404	15
α-helix	412-427	16
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	491-508	18

Chain D: 26 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
β-strand	20-25	6	1
α-helix	28-31	4
β-strand	35-38	4	1
β-strand	46-54	9	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	94-95	2	22
β-strand	101	1	22
β-strand	113-115	3	21
α-helix	119-122	4
α-helix	123-125	3
β-strand	132-133	2	23
α-helix	138-143	6
β-strand	146-147	2	23
β-strand	151-156	6	22
α-helix	162-169	8
α-helix	170-174	5
β-strand	180-186	7	22
α-helix	190-202	13
β-strand	215-220	6	22
α-helix	226-246	21
β-strand	250-256	7	22
α-helix	259-269	11
α-helix	270-272	3
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
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	24
α-helix	337-340	4
β-strand	348	1	24
β-strand	354-355	2	22
α-helix	360-363	4
α-helix	365-391	27
α-helix	400-413	14
α-helix	419-421	3
α-helix	422-425	4
α-helix	434-445	12
α-helix	454-457	4
α-helix	464-474	11

Chain E: 23 helices, 25 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	70	1	2
β-strand	74-77	4	1
β-strand	83-85	3	25
α-helix	88-90	3
β-strand	94-95	2	26
β-strand	101	1	26
β-strand	113-115	3	25
α-helix	119-122	4
α-helix	123-125	3
β-strand	126	1	27
β-strand	132-133	2	28
α-helix	138-143	6
β-strand	146-147	2	28
β-strand	151-155	5	26
α-helix	162-176	15
β-strand	181-188	8	26
α-helix	190-203	14
β-strand	215-221	7	26
α-helix	226-245	20
β-strand	250-256	7	26
α-helix	258-271	14
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	298	1	26
β-strand	299	1	27
β-strand	303-309	7	26
α-helix	313-315	3
α-helix	320-326	7
β-strand	331-334	4	26
β-strand	335	1	29
α-helix	337-341	5
β-strand	348	1	29
β-strand	354-355	2	26
α-helix	365-383	19
α-helix	388-391	4
α-helix	398-413	16
α-helix	422-425	4
α-helix	428-429	2
α-helix	434-446	13
α-helix	454-456	3
α-helix	464-471	8

Chain F: 26 helices, 25 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	70	1	9
β-strand	74-77	4	1
β-strand	83-86	4	30
α-helix	88-90	3
β-strand	91	1	31
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	132-133	2	32
α-helix	138-143	6
β-strand	146-147	2	32
β-strand	151-156	6	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	226-245	20
β-strand	250-256	7	31
α-helix	259-269	11
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	299	1	33
β-strand	302	1	33
β-strand	303-311	9	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	365-391	27
α-helix	393-395	3
α-helix	398-413	16
α-helix	419-421	3
α-helix	422-425	4
α-helix	434-445	12
α-helix	454-457	4
α-helix	463-472	10

Chain G: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-36	34
α-helix	39-41	3
α-helix	43-46	4
β-strand	69-71	3	35
α-helix	82-87	6
β-strand	106-108	3	35
α-helix	110-115	6
β-strand	128	1	35
α-helix	135-137	3
α-helix	138-146	9
β-strand	160-161	2	35
β-strand	164-165	2	36
β-strand	171-172	2	36
α-helix	205-271	67

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATP synthase alpha chain heart isoform, mitochondrial precursor	A, B, C	protein	510	BOS TAURUS	P19483 (AlphaFold model)
ATP synthase beta chain, mitochondrial precursor	D, E, F	protein	482	BOS TAURUS	P00829 (AlphaFold model)
ATP synthase gamma chain, mitochondrial precursor	G	protein	272	BOS TAURUS	P05631 (AlphaFold model)

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

>1W0J_1 ATP SYNTHASE ALPHA CHAIN HEART ISOFORM, MITOCHONDRIAL PRECURSOR (chains A, B, C)
QKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLK
GMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGP
IGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAA
PLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFY
LHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKG
IRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSR
GVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALL
GKIRTDGKISEESDAKLKEIVTNFLAGFEA

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

>1W0J_2 ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (chains D, E, F)
AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGES
TVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAI
HAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA
HGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTG
LTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERI
TTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSR
IMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQ
PFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEE
HS

Sequence of entity 3 (G), FASTA

>1W0J_3 ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAAL

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
BEF	Beryllium trifluoride ion	Be F3	2
MG	Magnesium ion	Mg	5
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5

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

Primary citation

The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride. Kagawa, R., Montgomery, M.G., Braig, K. et al. EMBO J (2004) 23:2734. DOI 10.1038/SJ.EMBOJ.7600293 · 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…
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
2JJ1 2.7 Å, The Structure of F1-ATPase inhibited by piceatannol.

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