PDB-5bqj: Structure of the yeast F1FO ATPase C10 ring with 21-hydroxy-oligomycin

ID or keywords:

Entry

Database: PDB / ID: 5bqj

Title

Structure of the yeast F1FO ATPase C10 ring with 21-hydroxy-oligomycin

Components

ATP synthase subunit 9, mitochondrial

Keywords

MEMBRANE PROTEIN/ANTIBIOTIC / C10 ring / F1FO ATP synthase / 21-hydroxy-oligomycin / mitochondria / membrane / protein-antibiotic complex / MEMBRANE PROTEIN-ANTIBIOTIC complex

Function / homology

Function and homology information

: / : / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / 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 21-hydroxy-oligomycin
Authors: Mueller, D.M.

History

Deposition	May 29, 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 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5bqj.cif.gz	288.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5bqj.ent.gz	241 KB	Display	PDB format
PDBx/mmJSON format	5bqj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5bqj_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	5bqj_full_validation.pdf.gz	2.9 MB	Display
Data in XML	5bqj_validation.xml.gz	29.9 KB	Display
Data in CIF	5bqj_validation.cif.gz	41.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/5bqj ftp://data.pdbj.org/pub/pdb/validation_reports/bq/5bqj	HTTPS FTP

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Related structure data

Related structure data	4f4sS 5bps 5bq6 5bqa S: Starting model for refinement
Similar structure data	5bqa-2 4f4s-2 5bps-1 3zry-2 5bps-2 4f4s-1 5bq6-2 5bqa-1 3u32-1 3u2y-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

83.6 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
84.4 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.975, 75.975, 489.218
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-E21 / 21-hydroxy-oligomycin Mass: 807.062 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄₅H₇₄O₁₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.28 Å³/Da / Density % sol: 46.07 %
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: Jul 16, 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: 42710 / Num. obs: 42710 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 19.6 Å² / R_merge(I) obs: 0.094 / Net I/σ(I): 18.8
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 4 % / R_merge(I) obs: 0.511 / % 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: 0.95 / Cor.coef. F_o:F_c free: 0.921 / SU B: 9.019 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23718	2155	5 %	RANDOM
R_work	0.19862	-	-	-
obs	0.20055	40537	99.62 %	-

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: 29.659 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1 Å²	0 Å²	0 Å²
2-	-	1 Å²	0 Å²
3-	-	-	-2 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5299	0	399	129	5827

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	6023
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.263	2.068	8260
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.824	5	831
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.102	23.101	129
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.97	15	896
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.71	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	1125
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: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.247	140	-
R_work	0.216	2642	-
obs	-	-	99.82 %

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	0.8472	0.0381	-2.0871	0.6439	-1.0893	20.5708	0.0039	-0.2083	0.1158	0.1416	0.0648	-0.0653	-0.3354	0.3126	-0.0687	0.0334	0.0146	-0.0255	0.0618	-0.0266	0.0917	48.3265	8.3734	31.985
2	0.6767	-0.0458	-1.4874	0.3501	-0.9703	21.18	-0.0617	-0.2225	0.0401	0.1385	0.0092	-0.1046	-0.1321	0.8472	0.0524	0.1217	-0.0273	-0.0265	0.1199	-0.0417	0.1801	50.9054	16.1799	28.0408
3	0.8143	0.134	-1.1957	0.711	-1.989	18.4585	0.0907	-0.181	0.1203	0.1757	0.1226	0.0183	-0.3665	0.1216	-0.2133	0.0529	0.0189	-0.004	0.0776	-0.0264	0.1028	41.4239	12.858	31.962
4	0.7478	-0.0445	-0.7998	0.476	-1.1119	17.8105	0.0399	-0.2244	0.15	0.1885	0.0158	-0.0369	-0.8753	0.3085	-0.0557	0.1548	-0.0164	0.0052	0.0679	-0.0452	0.1709	38.8899	20.7656	28.5111
5	0.9264	0.2044	0.1649	0.7043	-1.9569	22.8931	0.1401	-0.1885	0.068	0.1941	0.1281	0.118	-0.254	-0.0972	-0.2682	0.067	0.0232	0.0195	0.0954	-0.0066	0.1003	33.1837	12.4406	32.0887
6	0.6326	0.0568	0.1755	0.651	-2.0547	24.8899	-0.1205	-0.1793	0.1093	0.1925	-0.1041	0.002	-0.7332	-0.1318	0.2246	0.1183	0.0327	0.0032	0.0909	-0.0259	0.1676	26.5658	17.2456	28.4493
7	0.9003	-0.1621	1.1972	0.785	-1.8274	20.5194	0.0702	-0.1968	-0.0057	0.1747	0.1229	0.0861	-0.1336	-0.2212	-0.1931	0.0544	0.0101	0.0113	0.0578	-0.0019	0.0972	26.8423	7.2129	32.0011
8	0.5976	-0.0933	0.5292	0.2985	-0.8453	18.719	-0.0609	-0.1635	0.0893	0.136	-0.0585	0.0608	-0.5785	-0.6184	0.1195	0.0809	0.0128	0.0379	0.1414	-0.0147	0.1665	18.6261	7.2912	28.2192
9	0.8157	-0.251	2.1418	0.8502	-1.1111	28.6659	0.0489	-0.207	-0.0922	0.1923	0.2156	0.1478	-0.0198	-0.4045	-0.2645	0.0582	0.0261	0.034	0.0878	0.0278	0.1072	24.6888	-0.7219	32.1416
10	0.6353	-0.2332	3.0993	0.6383	0.4149	19.748	-0.0982	-0.1973	-0.0168	0.2087	-0.0214	0.126	0.0333	-1.115	0.1195	0.074	-0.0209	0.0239	0.1782	0.019	0.1741	17.9754	-5.5241	28.144
11	1.0293	0.216	1.6772	0.8977	1.3158	16.3012	0.2277	-0.2777	-0.0831	0.2419	0.0242	0.033	0.3721	-0.0211	-0.2519	0.0999	-0.0497	0.0085	0.0926	0.0151	0.0845	-8.4346	27.6806	31.992
12	0.8025	-0.2127	0.1262	0.6675	1.1952	17.0155	-0.158	-0.22	-0.0776	0.2685	-0.1984	0.0213	0.4584	-0.3845	0.3564	0.1543	-0.0711	0.0176	0.1794	0.0458	0.1691	-9.331	19.425	28.7553
13	0.5614	0.3928	1.1757	1.0387	2.2659	22.4258	0.1591	-0.2517	-0.1004	0.268	-0.0265	-0.0921	0.313	-0.0084	-0.1326	0.0834	-0.0437	-0.0251	0.145	0.0481	0.1118	-0.8306	24.7412	31.9118
14	0.8388	-0.1622	0.2957	0.5073	2.5669	19.1088	-0.1333	-0.2901	-0.0957	0.2648	-0.0281	-0.0275	0.9438	-0.0898	0.1614	0.1959	-0.0259	-0.0385	0.1567	0.0795	0.2042	3.2142	17.4525	28.8383
15	0.5346	0.2218	-0.1649	0.8432	2.2691	19.4112	0.1888	-0.2711	-0.1269	0.2574	0.0073	-0.1047	0.3234	0.2773	-0.1961	0.1108	-0.0632	-0.0509	0.1586	0.0636	0.1014	7.1408	26.7662	32.2816
16	1.1782	0.2986	-0.4948	1.1265	3.2909	23.2596	0.0578	-0.3454	-0.1579	0.3699	-0.0902	-0.1789	0.9156	0.2061	0.0324	0.1473	0.0109	-0.0584	0.1482	0.0742	0.1875	14.7288	23.4757	28.2371
17	0.9018	0.2065	-1.0846	0.815	1.5285	18.7175	0.19	-0.3048	-0.0449	0.2784	0.0028	-0.0935	0.4727	0.1235	-0.1927	0.1133	-0.0479	-0.0406	0.1287	0.0358	0.1133	12.4634	33.1184	32.7265
18	1.225	0.1914	-1.3836	0.743	0.7381	16.7164	0.0547	-0.3337	-0.0718	0.2589	-0.0846	-0.1056	0.3562	0.8266	0.0299	0.0953	-0.0186	-0.0564	0.1482	0.0428	0.1543	20.4917	34.6739	28.8539
19	1.1109	0.0403	-2	0.592	0.4433	17.0144	0.2114	-0.2961	0.0093	0.1879	0.0269	-0.1435	-0.0227	0.139	-0.2382	0.0978	-0.0524	-0.0482	0.098	0.0061	0.1003	12.9275	41.4142	32.3927
20	0.9209	-0.0066	-2.3151	0.8146	-0.8202	20.2852	0.019	-0.3158	-0.0066	0.243	-0.1226	-0.0293	-0.057	0.8932	0.1036	0.1064	-0.0836	-0.0288	0.1827	0.0173	0.1583	18.4891	47.4394	28.7738

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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