PDB-5bq6: Structure of the yeast F1FO ATPase C10 ring with oligomycin B

ID or keywords:

Entry

Database: PDB / ID: 5bq6

Title

Structure of the yeast F1FO ATPase C10 ring with oligomycin B

Components

ATP synthase subunit 9, mitochondrial

Keywords

MEMBRANE PROTEIN/ANTIBIOTIC / C10 ring / F1FO ATP synthase / oligomycin B / 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: 2.3 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 B
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

-
Download

PDBx/mmCIF format	5bq6.cif.gz	282.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5bq6.ent.gz	235.7 KB	Display	PDB format
PDBx/mmJSON format	5bq6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5bq6_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	5bq6_full_validation.pdf.gz	2.9 MB	Display
Data in XML	5bq6_validation.xml.gz	30.4 KB	Display
Data in CIF	5bq6_validation.cif.gz	40.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/5bq6 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/5bq6	HTTPS FTP

-
Related structure data

Related structure data	4f4sS 5bps 5bqa 5bqj S: Starting model for refinement
Similar structure data	5bqj-2 5bqa-2 4f4s-2 6a02-1 5bqa-1 6a09-4 5bps-2 6a09-3 3u32-1 5bqj-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

-
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

83.5 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
84.3 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
82.7 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.293, 76.293, 488.558
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-EFB / oligomycin B Mass: 805.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄₅H₇₂O₁₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.45 %
Crystal grow	Temperature: 278 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

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 1, 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: 2.3→50 Å / Num. all: 32630 / Num. obs: 32630 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / B_iso Wilson estimate: 23 Å² / R_merge(I) obs: 0.088 / Net I/σ(I): 20.3
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.39 / % possible all: 98.7

-
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: 2.3→50 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.925 / SU B: 12.456 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24713	1657	5.1 %	RANDOM
R_work	0.20396	-	-	-
obs	0.20615	30963	98.97 %	-

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: 32.137 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.01 Å²	0 Å²	0 Å²
2-	-	1.01 Å²	0 Å²
3-	-	-	-2.02 Å²

Refinement step

Cycle: 1 / Resolution: 2.3→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5297	0	399	94	5790

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	5849
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.324	2.069	7960
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.108	5	747
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.519	23.101	129
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.308	15	857
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.781	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1074
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3939
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: 2.303→2.363 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.255	106	-
R_work	0.205	1962	-
obs	-	-	96.73 %

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	0.7152	0.0497	-1.8278	0.8544	-1.1256	19.3871	-0.0071	-0.1942	0.1388	0.1761	0.0788	-0.0343	-0.1132	0.3212	-0.0717	0.04	0.0173	-0.023	0.0671	-0.0269	0.1	48.485	8.4711	31.9502
2	0.4799	-0.2549	-1.1629	0.5991	-1.0034	20.7841	-0.1287	-0.1965	0.0041	0.217	-0.0582	-0.087	-0.3189	0.8953	0.187	0.1091	-0.014	-0.0191	0.1483	-0.0032	0.177	50.9957	16.3168	27.9998
3	0.8024	-0.0676	-0.6973	0.9498	-2.574	19.9099	0.0697	-0.1853	0.1682	0.1833	0.0844	0.0466	-0.1341	0.1505	-0.1541	0.0649	0.0036	0.0155	0.0501	-0.0293	0.1063	41.5214	12.905	31.9533
4	0.607	-0.3694	0.1606	0.9352	-1.8473	17.127	-0.0977	-0.2092	0.153	0.2437	-0.0625	-0.0025	-0.7417	0.3699	0.1602	0.0867	-0.016	0.0085	0.1248	-0.059	0.1792	38.9056	20.8342	28.4849
5	0.9155	-0.0168	0.8193	0.6799	-2.1394	20.6947	0.0769	-0.172	0.0712	0.2257	0.101	0.1014	-0.1242	0.1116	-0.1779	0.1074	0.0431	0.0196	0.0712	-0.012	0.1215	33.2876	12.4275	32.0813
6	0.6543	-0.2568	1.4135	0.5471	-2.214	26.2689	-0.2395	-0.1771	0.0639	0.2335	-0.108	0.039	-0.8615	-0.2362	0.3475	0.132	0.0064	0.0201	0.1313	-0.0309	0.1911	26.5874	17.2299	28.5151
7	0.7376	0.225	0.7512	0.9284	-2.3043	20.9843	0.1146	-0.146	-0.0009	0.2149	0.1463	0.1424	-0.2559	-0.0324	-0.2608	0.0572	0.0279	0.0264	0.1099	0.0178	0.0969	26.9742	7.1409	31.9675
8	0.4849	0.3014	0.7884	0.3205	-0.6229	15.8086	0.0359	-0.1647	0.0604	0.115	-0.0251	0.099	-0.4473	-0.6502	-0.0108	0.0858	0.0634	0.043	0.1278	-0.0041	0.1884	18.7033	7.2288	28.1864
9	1.0603	-0.3407	2.3074	0.6782	0.1882	24.2152	0.0425	-0.2535	-0.111	0.1569	0.1851	0.154	0.2565	-0.1734	-0.2277	0.0536	0.0182	0.0397	0.0826	0.035	0.1065	24.8114	-0.8413	32.121
10	0.4613	-0.0734	2.8125	0.7815	0.234	24.7114	-0.0799	-0.2059	0.0599	0.1893	-0.1388	0.1201	0.1013	-1.005	0.2187	0.0737	0.0136	0.0009	0.1821	0.005	0.2039	18.0874	-5.6411	28.1472
11	0.85	0.1191	1.0902	1.1844	1.6125	15.5403	0.2379	-0.3493	-0.1169	0.2379	-0.0079	0.0326	0.1728	0.1269	-0.23	0.1157	-0.1106	-0.0047	0.1738	0.0216	0.0941	-8.4787	27.8419	31.9536
12	0.4715	-0.2682	-0.0678	0.9583	1.552	21.5775	-0.0381	-0.2108	-0.0696	0.2932	-0.2155	0.0148	0.344	-0.5675	0.2536	0.1096	-0.1016	0.006	0.2322	0.0514	0.1822	-9.4622	19.6113	28.7114
13	0.5925	0.1429	0.3704	1.0312	2.3702	22.7889	0.2415	-0.3164	-0.1263	0.2846	0.017	-0.1032	0.3216	-0.0421	-0.2584	0.1575	-0.1056	-0.0458	0.177	0.059	0.1376	-0.8165	24.7994	32.2193
14	0.9177	-0.1778	-1.2648	0.6778	3.0643	14.4391	-0.2012	-0.2615	-0.1139	0.2682	-0.0988	0.0357	1.0852	-0.083	0.3001	0.2336	-0.0742	-0.0375	0.1642	0.0694	0.2339	3.1426	17.5856	28.7939
15	0.8409	0.0723	-0.896	0.6896	2.901	18.1209	0.2268	-0.3044	-0.112	0.2231	-0.0189	-0.1285	0.3822	0.3232	-0.2079	0.1397	-0.0749	-0.0639	0.1163	0.0622	0.1374	7.108	26.8896	32.2465
16	1.0204	0.1851	-0.5503	1.0957	3.3592	25.4889	-0.0318	-0.3844	-0.1009	0.3778	-0.1434	-0.0306	1.0481	0.1718	0.1752	0.1472	-0.0192	-0.0267	0.1618	0.0725	0.1995	14.7075	23.5357	28.2312
17	0.9812	-0.0039	-1.667	0.7166	2.3298	19.6063	0.166	-0.3099	-0.038	0.2715	-0.002	-0.1388	0.6334	-0.013	-0.164	0.1307	-0.0549	-0.0565	0.1336	0.0235	0.1161	12.4386	33.2608	32.5886
18	1.045	0.2731	-0.9244	0.8567	1.2411	15.7978	0.1135	-0.3612	-0.1142	0.2421	-0.0523	-0.0688	0.3945	0.9422	-0.0612	0.0753	-0.0262	-0.0515	0.1527	0.0483	0.1761	20.527	34.743	28.798
19	1.0517	0.4335	-2.0536	0.7532	-0.7066	14.1849	0.2164	-0.2695	0.0522	0.2098	0.0255	-0.0951	0.0827	0.0377	-0.242	0.0917	-0.0539	-0.0276	0.1406	-0.0017	0.1054	12.9164	41.4212	31.4303
20	0.7514	0.0731	-1.389	0.6449	-0.1493	17.3067	0.0327	-0.3093	0.0158	0.2477	-0.1843	-0.0641	-0.1512	0.6182	0.1516	0.1214	-0.0988	-0.0139	0.1937	0.0208	0.1784	18.5546	47.5541	28.7303

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	2 - 41
20	X-RAY DIFFRACTION	20	O	42 - 75

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi