PDB-5bps: Structure of the yeast F1FO ATPase C10 ring with oligomycin A

ID or keywords:

Entry

Database: PDB / ID: 5bps

Title

Structure of the yeast F1FO ATPase C10 ring with oligomycin A

Components

ATP synthase subunit 9, mitochondrial

Keywords

MEMBRANE PROTEIN/ANTIBIOTIC / C10 ring / F1FO ATP synthase / oligomycin A / mitochondria / membrane / protein-antibiotic complex / MEMBRANE PROTEIN-ANTIBIOTIC complex

Function / homology

Function and homology information

proton-transporting ATP synthase complex / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / : / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / mitochondrion / identical protein binding / cytosol
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.1 Å

Authors

Symersky, J. / Xu, T. / Mueller, D.M.

Citation

Journal: To be Published
Title: Structure of the yeast F1FO ATPase C10 ring with oligomycin A
Authors: Mueller, D.M.

History

Deposition	May 28, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5bps.cif.gz	288.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5bps.ent.gz	241.3 KB	Display	PDB format
PDBx/mmJSON format	5bps.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bp/5bps ftp://data.pdbj.org/pub/pdb/validation_reports/bp/5bps	HTTPS FTP

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Related structure data

Related structure data	4f4sS 5bq6 5bqa 5bqj S: Starting model for refinement
Similar structure data	4f4s-1 5bqa-1 5bqj-1 5bqa-2 4f4s-2 5bqj-2 5bq6-2 3u32-1 3zry-2 5bq6-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#219 - Mar 2018 Vacuolar ATPase similarity (7) #72 - Dec 2005 ATP Synthase similarity (7)

Deposited unit

A: ATP synthase subunit 9, mitochondrial

B: ATP synthase subunit 9, mitochondrial

C: ATP synthase subunit 9, mitochondrial

D: ATP synthase subunit 9, mitochondrial

E: ATP synthase subunit 9, mitochondrial

K: ATP synthase subunit 9, mitochondrial

L: ATP synthase subunit 9, mitochondrial

M: ATP synthase subunit 9, mitochondrial

N: ATP synthase subunit 9, mitochondrial

O: ATP synthase subunit 9, mitochondrial

hetero molecules

83.4 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP synthase subunit 9, mitochondrial

B: ATP synthase subunit 9, mitochondrial

C: ATP synthase subunit 9, mitochondrial

D: ATP synthase subunit 9, mitochondrial

E: ATP synthase subunit 9, mitochondrial

hetero molecules

A: ATP synthase subunit 9, mitochondrial

B: ATP synthase subunit 9, mitochondrial

C: ATP synthase subunit 9, mitochondrial

D: ATP synthase subunit 9, mitochondrial

E: ATP synthase subunit 9, mitochondrial

hetero molecules

defined by author&software
82.7 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

K: ATP synthase subunit 9, mitochondrial

L: ATP synthase subunit 9, mitochondrial

M: ATP synthase subunit 9, mitochondrial

N: ATP synthase subunit 9, mitochondrial

O: ATP synthase subunit 9, mitochondrial

hetero molecules

K: ATP synthase subunit 9, mitochondrial

L: ATP synthase subunit 9, mitochondrial

M: ATP synthase subunit 9, mitochondrial

N: ATP synthase subunit 9, mitochondrial

O: ATP synthase subunit 9, mitochondrial

hetero molecules

defined by author&software
84.2 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.216, 76.216, 489.190
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

#1: Protein	ATP synthase subunit 9, mitochondrial / Lipid-binding protein / Oligomycin resistance protein 1 Mass: 7790.385 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P61829, Hydrolases; Acting on acid anhydrides
#2: Chemical	ChemComp-EFO / Oligomycin A / (1R,4E,5'S,6S,6'S,7R,8S,10R,11R,12S,14R,15S,16R,18E,20E,22R,25S,27R,28S,29R)-22-ethyl-7,11,14,15-tetrahydroxy-6'-[(2R)-2-hydroxypropyl]-5',6,8,10,12,14,16,28,29-nonamethyl-3',4',5',6'-tetrahydro-3H,9H,13H-spiro[2,26-dioxabicyclo[23.3.1]nonacosa-4,18,20-triene-27,2'-pyran]-3,9,13-trione Mass: 791.062 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄₅H₇₄O₁₁ / Comment: antibiotic*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.41 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2012
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. all: 42953 / Num. obs: 42953 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 18.6 Å² / R_merge(I) obs: 0.091 / R_sym value: 0.091 / Net I/σ(I): 18.2
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 4 % / R_merge(I) obs: 0.435 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
HKL-2000		data scaling
REFMAC	5.6.0117	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: PDB entry 4F4S

4f4s

Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.924 / SU B: 8.617 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23867	2163	5 %	RANDOM
R_work	0.20098	-	-	-
obs	0.20285	40744	99.75 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 27.825 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.61 Å²	0 Å²	0 Å²
2-	-	0.61 Å²	0 Å²
3-	-	-	-1.22 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5296	0	392	143	5831

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	6013
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.26	2.067	8242
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.842	5	831
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.475	23.101	129
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.716	15	894
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.209	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1117
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	4079
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.102→2.157 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.262	144	-
R_work	0.212	2663	-
obs	-	-	99.26 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.8212	-0.0038	-2.0604	0.7615	-1.1138	16.9404	0.105	-0.1931	0.1087	0.1296	0.1868	-0.0965	-0.3367	0.1249	-0.2918	0.0367	0.0055	-0.0094	0.0922	-0.0369	0.0945	48.4126	8.4837	31.867
2	0.3692	-0.1175	-1.7276	0.8913	-0.9975	18.5174	0.046	-0.2245	0.0488	0.1726	0.0457	-0.1098	-0.3382	0.9376	-0.0917	0.054	-0.0377	-0.0264	0.1411	-0.0349	0.1642	50.9128	16.3408	27.9283
3	0.8324	-0.0641	-1.6341	0.9414	-2.3125	19.1758	0.1031	-0.1919	0.1026	0.1454	0.1791	0.0212	-0.1832	0.0853	-0.2822	0.0569	0.0089	0.0025	0.0736	-0.0194	0.0996	41.4765	12.9128	31.8582
4	0.7571	-0.0789	-0.2312	0.8263	-1.766	15.7942	-0.0279	-0.2174	0.1326	0.159	0.0324	-0.0472	-0.4722	0.1793	-0.0045	0.0666	-0.0045	-0.0052	0.069	-0.0371	0.1494	38.8621	20.7855	28.4215
5	0.8771	0.0703	-0.5146	0.8958	-1.9865	22.1429	0.1969	-0.1948	0.0623	0.176	0.2138	0.1545	-0.1116	0.194	-0.4106	0.0794	0.0121	0.0279	0.1207	0.0069	0.0911	33.2317	12.3818	32.001
6	1.0088	-0.0191	0.5862	0.4787	-2.3564	21.4237	-0.0302	-0.2207	0.0551	0.2032	0.0355	0.0239	-0.9014	-0.2439	-0.0053	0.0994	0.0303	-0.0003	0.06	-0.0301	0.153	26.5906	17.1322	28.3753
7	0.8251	-0.1817	0.6895	0.9465	-2.1774	17.0536	0.1083	-0.1782	-0.0135	0.1805	0.1508	0.1373	-0.1657	-0.02	-0.2591	0.0629	0.0087	0.0253	0.0655	0.008	0.0861	26.9557	7.103	31.8876
8	0.5821	0.0689	0.9206	0.2896	-0.7561	18.0944	-0.0075	-0.1448	0.0659	0.1214	-0.0067	0.1232	-0.5787	-0.6107	0.0142	0.0641	0.0295	0.0313	0.1206	0.0016	0.159	18.7428	7.165	28.1155
9	0.6989	-0.1436	2.22	0.942	-0.7128	20.954	0.0549	-0.2015	-0.0593	0.1707	0.2409	0.1648	-0.0403	-0.2417	-0.2958	0.0415	0.0184	0.0293	0.1195	0.0292	0.1055	24.805	-0.8655	32.0373
10	0.5679	0.0571	2.2763	0.8423	0.1854	21.4467	-0.0695	-0.2399	-0.0278	0.1451	-0.0032	0.1495	-0.1269	-0.7901	0.0727	0.0493	0.0109	0.0296	0.1537	0.0266	0.1623	18.133	-5.6689	28.0585
11	0.9866	0.2963	0.8924	0.914	1.2073	12.1545	0.2369	-0.337	-0.0899	0.2295	-0.0225	0.0371	0.3382	0.142	-0.2143	0.0903	-0.0738	0.0016	0.1567	0.0291	0.085	-8.4944	27.8405	31.965
12	0.6814	-0.0485	-0.3149	0.9657	1.6387	18.816	-0.0317	-0.2763	-0.0589	0.2656	-0.168	0.0183	0.284	-0.3256	0.1997	0.116	-0.0761	-0.003	0.1917	0.0537	0.1496	-9.4643	19.5947	28.7426
13	0.6278	0.282	1.3096	1.2449	2.1361	20.6348	0.2428	-0.337	-0.1306	0.2325	0.0293	-0.0703	0.1594	-0.1249	-0.2721	0.1221	-0.1183	-0.0414	0.2157	0.0718	0.0988	-0.9097	24.8815	31.8952
14	0.7175	-0.1815	-0.4714	0.3357	1.6088	17.5052	-0.0287	-0.3011	-0.145	0.2105	-0.0384	0.0088	0.7715	0.1915	0.0671	0.1629	-0.0849	-0.0373	0.2038	0.0944	0.1924	3.0373	17.5994	28.772
15	0.6043	-0.0769	-0.3546	1.0422	2.4215	22.8216	0.2161	-0.3345	-0.0999	0.2178	0.0145	-0.066	0.1359	0.3023	-0.2305	0.1379	-0.1288	-0.0532	0.2003	0.0879	0.1036	7.0723	26.8559	32.268
16	1.291	-0.0871	-0.3294	1.1096	2.7985	20.5446	0.057	-0.4412	-0.1512	0.3426	-0.0758	-0.0957	0.9789	0.2021	0.0188	0.1153	-0.0495	-0.0531	0.181	0.0946	0.1762	14.6462	23.5175	28.247
17	0.8671	-0.1641	-1.3285	0.7435	2.1287	14.8311	0.1887	-0.3203	-0.0417	0.2211	-0.0293	-0.0963	0.3674	-0.0073	-0.1594	0.1329	-0.1035	-0.0497	0.1515	0.0557	0.1091	12.4144	33.1648	32.7227
18	0.8588	0.1516	-0.6345	0.6114	1.4415	16.8687	0.0774	-0.3088	-0.0772	0.2151	-0.0419	-0.1088	0.5488	0.5949	-0.0355	0.0832	-0.0391	-0.0513	0.1683	0.062	0.1522	20.431	34.6974	28.8475
19	0.9442	0.0816	-2.1573	0.8339	0.05	11.8141	0.1769	-0.3112	0.0045	0.1906	0.0275	-0.1033	0.1258	0.0433	-0.2045	0.1022	-0.0944	-0.0357	0.1783	0.0276	0.0993	12.95	41.4895	32.3781
20	0.7757	0.2713	-2.1638	1.0986	-0.9286	23.2022	0.0698	-0.3276	0.02	0.2285	-0.1453	-0.0698	0.0884	0.6494	0.0754	0.0763	-0.0747	-0.0272	0.195	0.0064	0.1337	18.4987	47.4477	28.7412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 41
2	X-RAY DIFFRACTION	2	A	42 - 74
3	X-RAY DIFFRACTION	3	B	1 - 41
4	X-RAY DIFFRACTION	4	B	42 - 75
5	X-RAY DIFFRACTION	5	C	1 - 41
6	X-RAY DIFFRACTION	6	C	42 - 75
7	X-RAY DIFFRACTION	7	D	1 - 41
8	X-RAY DIFFRACTION	8	D	42 - 74
9	X-RAY DIFFRACTION	9	E	1 - 41
10	X-RAY DIFFRACTION	10	E	42 - 74
11	X-RAY DIFFRACTION	11	K	1 - 41
12	X-RAY DIFFRACTION	12	K	42 - 75
13	X-RAY DIFFRACTION	13	L	1 - 41
14	X-RAY DIFFRACTION	14	L	42 - 75
15	X-RAY DIFFRACTION	15	M	1 - 41
16	X-RAY DIFFRACTION	16	M	42 - 75
17	X-RAY DIFFRACTION	17	N	1 - 41
18	X-RAY DIFFRACTION	18	N	42 - 75
19	X-RAY DIFFRACTION	19	O	1 - 41
20	X-RAY DIFFRACTION	20	O	42 - 75

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