1NBM: F1-atpase

The structure of bovine F1-atpase covalently inhibited with 4-chloro-7-nitrobenzofurazan. Determined by X-ray diffraction at 3.0 Å resolution. Released 26 Aug 1998.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Bos taurus
Chains: 7
Atoms: 23,057
Mol. weight: 353.49 kDa
Ligands: MG, ATP, ADP, PO4
Released: 26 Aug 1998

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

Secondary structure: helices and β-sheets

1NBM contains 149 α-helices and 162 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: 24 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	28-35	8	1
β-strand	38-43	6	1
β-strand	48	1	2
β-strand	51-54	4	1
β-strand	60-67	8	1
β-strand	70-75	6	1
α-helix	79-81	3
β-strand	87-90	4	1
β-strand	96-99	4	3
α-helix	101-103	3
β-strand	107-109	3	4
β-strand	114	1	4
β-strand	125-128	4	3
α-helix	132-135	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	166-169	4	7
α-helix	175-185	11
α-helix	187-191	5
β-strand	200-207	8	4
α-helix	210-222	13
α-helix	225-228	4
β-strand	229-235	7	4
α-helix	240-259	20
β-strand	263-269	7	4
α-helix	271-284	14
α-helix	287-288	2
β-strand	289	1	8
α-helix	291-293	3
β-strand	295	1	8
α-helix	298-306	9
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	375-378	4
α-helix	381-404	24
α-helix	412-427	16
α-helix	435-437	3
α-helix	438-449	12
α-helix	458-475	18
α-helix	477-486	10
α-helix	491-508	18

Chain B: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	28-35	8	9
β-strand	38-43	6	9
α-helix	47	1
β-strand	48	1	10
β-strand	51-55	5	9
β-strand	60-66	7	9
β-strand	71-75	5	9
α-helix	79-81	3
β-strand	87-94	8	9
β-strand	96-99	4	11
α-helix	101-103	3
β-strand	107-109	3	12
β-strand	114	1	12
β-strand	125-128	4	11
α-helix	131-134	4
β-strand	139	1	13
β-strand	145	1	14
α-helix	151-156	6
β-strand	160	1	14
β-strand	164	1	12
β-strand	166-169	4	15
α-helix	175-185	11
α-helix	187-190	4
β-strand	200-206	7	12
α-helix	210-222	13
α-helix	225-228	4
β-strand	229-234	6	12
α-helix	240-258	19
β-strand	263-269	7	12
α-helix	271-284	14
β-strand	289	1	16
α-helix	291-293	3
β-strand	295	1	16
α-helix	298-307	10
β-strand	311	1	12
β-strand	312	1	13
α-helix	314-316	3
β-strand	320-325	6	12
β-strand	326-328	3	15
α-helix	337-343	7
β-strand	348-352	5	15
α-helix	354-358	5
β-strand	365	1	15
β-strand	371-372	2	15
α-helix	376-378	3
α-helix	381-384	4
α-helix	387-399	13
α-helix	412-428	17
α-helix	438-450	13
α-helix	458-474	17
α-helix	477-486	10
α-helix	491-505	15

Chain C: 26 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	28-35	8	9
β-strand	38-43	6	9
α-helix	47	1
β-strand	48	1	17
β-strand	51-55	5	9
β-strand	60-66	7	9
β-strand	71-75	5	9
α-helix	79-81	3
β-strand	87-94	8	9
β-strand	96-99	4	18
α-helix	101-103	3
β-strand	107-109	3	19
β-strand	114	1	19
β-strand	125-128	4	18
α-helix	132-134	3
β-strand	139	1	20
β-strand	145	1	21
α-helix	151-156	6
β-strand	160	1	21
β-strand	164	1	19
β-strand	166-169	4	22
α-helix	175-185	11
α-helix	187-190	4
α-helix	195-197	3
β-strand	200-206	7	19
α-helix	210-222	13
α-helix	226-228	3
β-strand	229-234	6	19
α-helix	240-258	19
β-strand	263-269	7	19
α-helix	271-284	14
β-strand	290	1	23
β-strand	293	1	23
α-helix	298-306	9
β-strand	311	1	19
β-strand	312	1	20
α-helix	314-316	3
β-strand	320-325	6	19
β-strand	326-328	3	22
β-strand	330	1	24
β-strand	333	1	24
α-helix	337-343	7
β-strand	348-352	5	22
α-helix	354-358	5
β-strand	365	1	22
α-helix	367-369	3
β-strand	371-372	2	22
α-helix	375-378	4
α-helix	381-386	6
α-helix	390-403	14
α-helix	412-427	16
α-helix	435-437	3
α-helix	438-449	12
α-helix	458-474	17
α-helix	477-486	10
α-helix	491-508	18

Chain D: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	9
β-strand	20-25	6	9
α-helix	29-31	3
β-strand	34-38	5	9
β-strand	46-54	9	9
β-strand	57-62	6	9
β-strand	70	1	17
β-strand	74-81	8	9
β-strand	83-85	3	25
α-helix	88-90	3
β-strand	91	1	26
β-strand	94-95	2	26
α-helix	96	1
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	152-156	5	26
α-helix	162-169	8
α-helix	170-174	5
β-strand	181-186	6	26
α-helix	190-202	13
β-strand	215-220	6	26
α-helix	226-244	19
β-strand	251-256	6	26
α-helix	259-271	13
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	299	1	27
β-strand	304-311	8	26
α-helix	313-315	3
α-helix	320-326	7
β-strand	331-334	4	26
β-strand	335	1	29
α-helix	337-342	6
β-strand	348	1	29
β-strand	354-355	2	26
α-helix	365-388	24
α-helix	398-414	17
α-helix	422-425	4
α-helix	434-445	12
α-helix	454-456	3
α-helix	463-472	10

Chain E: 25 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	46-51	6	1
β-strand	52	1	9
β-strand	57-62	6	1
β-strand	70	1	2
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	132-133	2	32
α-helix	138-143	6
α-helix	145	1
β-strand	146-147	2	32
β-strand	151-155	5	31
α-helix	162-177	16
β-strand	181-188	8	31
α-helix	190-203	14
β-strand	215-221	7	31
α-helix	226-242	17
α-helix	243-247	5
β-strand	250-255	6	31
α-helix	259-271	13
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-295	11
β-strand	298	1	31
β-strand	303-309	7	31
α-helix	313-315	3
α-helix	320-326	7
β-strand	331-334	4	31
β-strand	335	1	33
α-helix	337-341	5
β-strand	348	1	33
β-strand	355	1	31
α-helix	360-363	4
α-helix	365-387	23
α-helix	388-392	5
α-helix	398-413	16
α-helix	419-421	3
α-helix	422-425	4
α-helix	434-446	13
α-helix	454-457	4
α-helix	463-473	11

Chain F: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	9
β-strand	20-24	5	9
α-helix	29-31	3
β-strand	35-38	4	9
β-strand	46-54	9	9
β-strand	57-62	6	9
β-strand	70	1	10
β-strand	74-77	4	9
β-strand	83-86	4	34
β-strand	91	1	35
β-strand	94-95	2	35
β-strand	101	1	35
β-strand	112-115	4	34
α-helix	119-122	4
β-strand	126	1	36
β-strand	132-133	2	37
α-helix	138-143	6
β-strand	146-147	2	37
β-strand	151-156	6	35
α-helix	162-169	8
α-helix	170-174	5
β-strand	181-186	6	35
α-helix	190-203	14
β-strand	215-220	6	35
α-helix	226-229	4
α-helix	232-246	15
β-strand	251-256	6	35
α-helix	259-272	14
α-helix	274-276	3
α-helix	278-280	3
α-helix	285-293	9
β-strand	299	1	36
β-strand	302	1	36
β-strand	304-311	8	35
α-helix	313-315	3
α-helix	320-326	7
β-strand	331-334	4	35
β-strand	335	1	38
α-helix	336	1
α-helix	337-341	5
β-strand	348	1	38
β-strand	355	1	35
α-helix	360-363	4
α-helix	365-391	27
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	463-473	11

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-41	39
α-helix	82-89	8
α-helix	210-269	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
F1-atpase	A, B, C	protein	510	Bos taurus	P19483 (AlphaFold model)
F1-atpase	D, F	protein	480	Bos taurus	P00829 (AlphaFold model)
F1-atpase	E	protein	480	Bos taurus	P00829 (AlphaFold model)
F1-atpase	G	protein	272	Bos taurus	P05631 (AlphaFold model)

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

>1NBM_1 F1-ATPASE (chains A, B, C)
QKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLK
GMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGP
IGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAA
PLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFY
LHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKG
IRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSR
GVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALL
GKIRTDGKISEESDAKLKEIVTNFLAGFEA

Sequence of entity 2 (D, F), FASTA

>1NBM_2 F1-ATPASE (chains D, F)
AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGES
TVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAI
HAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA
HGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTG
LTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERI
TTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSR
IMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQ
PFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEE

Sequence of entity 3 (E), FASTA

>1NBM_3 F1-ATPASE (chains E)
AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGES
TVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAI
HAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA
HGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTG
LTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERI
TTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSR
IMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQ
PFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEE

Sequence of entity 4 (G), FASTA

>1NBM_4 F1-ATPASE (chains G)
ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTP
EDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTH
SDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFS
LDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS
EMIDKLTLTFNRTRQAVITKELIEIISGAAAL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
PO4	Phosphate ion	O4 P	1

Primary citation

Bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan: the structure provides further support for a rotary catalytic mechanism. Orriss, G.L., Leslie, A.G., Braig, K. et al. Structure (1998) 6:831-837. DOI 10.1016/S0969-2126(98)00085-9 · 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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