PDB-2cly: Subcomplex of the stator of bovine mitochondrial ATP synthase

ID or keywords:

Entry

Database: PDB / ID: 2cly

Title

Subcomplex of the stator of bovine mitochondrial ATP synthase

Components

ATP SYNTHASE B CHAIN, MITOCHONDRIAL
ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL
ATP SYNTHASE D CHAIN, MITOCHONDRIAL

Keywords

HYDROLASE /

MITOCHONDRIA /

MITOCHONDRION /

ION TRANSPORT / CF(0) /

STATOR / TRANSPORT /

ACETYLATION /

ATP SYNTHASE / HYDROGEN ION TRANSPORT / TRANSIT PEPTIDE / PERIPHERAL STALK

Function / homology

Function and homology information

Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase activity, rotational mechanism
Similarity search - Function

Biological species

BOS TAURUS (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.8 Å

Authors

Kane Dickson, V. / Silvester, J.A. / Fearnley, I.M. / Leslie, A.G.W. / Walker, J.E.

Citation

Journal: Embo J. / Year: 2006
Title: On the Structure of the Stator of the Mitochondrial ATP Synthase.
Authors: Kane Dickson, V. / Silvester, J.A. / Fearnley, I.M. / Leslie, A.G.W. / Walker, J.E.

History

Deposition	May 3, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 28, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2cly.cif.gz	133.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2cly.ent.gz	109.2 KB	Display	PDB format
PDBx/mmJSON format	2cly.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cl/2cly ftp://data.pdbj.org/pub/pdb/validation_reports/cl/2cly	HTTPS FTP

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Related structure data

Related structure data	1vzs
Similar structure data	5az4-1 5az4-3 5az4-4 4zi8-d 6iys-1 3i3n-d 218 4bsk-1 3i00-d 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 (14) #72 - Dec 2005 ATP Synthase similarity (3)

Deposited unit

A: ATP SYNTHASE B CHAIN, MITOCHONDRIAL

B: ATP SYNTHASE D CHAIN, MITOCHONDRIAL

C: ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL

D: ATP SYNTHASE B CHAIN, MITOCHONDRIAL

E: ATP SYNTHASE D CHAIN, MITOCHONDRIAL

F: ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL

105 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP SYNTHASE B CHAIN, MITOCHONDRIAL

B: ATP SYNTHASE D CHAIN, MITOCHONDRIAL

C: ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL

defined by author&software
52.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: ATP SYNTHASE B CHAIN, MITOCHONDRIAL

E: ATP SYNTHASE D CHAIN, MITOCHONDRIAL

F: ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL

defined by author&software
52.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	50.499, 79.354, 115.665
Angle α, β, γ (deg.)	90.00, 93.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	D
1	2	B
2	2	E
1	3	C
2	3	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	5 - 56
2	1	1	2	D	5 - 56
1	2	1	2	A	57 - 99
2	2	1	2	D	57 - 99
1	1	2	2	B	19 - 39
2	1	2	2	E	19 - 39
1	2	2	2	B	44 - 49
2	2	2	2	E	44 - 49
1	3	2	2	B	78 - 99
2	3	2	2	E	78 - 99
1	4	2	2	B	106 - 122
2	4	2	2	E	106 - 122
1	1	3	2	C	37 - 56
2	1	3	2	F	37 - 56
1	2	3	3	C	18 - 35
2	2	3	3	F	18 - 35

NCS ensembles :

ID
1
2
3

#1: Protein	ATP SYNTHASE B CHAIN, MITOCHONDRIAL Mass: 24702.709 Da / Num. of mol.: 2 / Fragment: STATOR SUBCOMPLEX Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Plasmid: PET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P13619, H+-transporting two-sector ATPase
#2: Protein	ATP SYNTHASE D CHAIN, MITOCHONDRIAL Mass: 18588.256 Da / Num. of mol.: 2 / Fragment: STATOR SUBCOMPLEX Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Plasmid: PET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P13620, H+-transporting two-sector ATPase
#3: Protein	ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL Mass: 9118.253 Da / Num. of mol.: 2 / Fragment: STATOR SUBCOMPLEX Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Plasmid: PET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P02721, H+-transporting two-sector ATPase
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUES 79-183 ONLY NO PRESEQUENCE, RESIDUES 5-70 NO INITIATOR METHIONINE, RESIDUES 3-123

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 61.5 % Description: SE MET STRUCTURE SOLVED USING SHARP. NATIVE STRUCTURE WHICH HAD A DIFFERENT UNIT CELL WAS SOLVED USING PHASER AND PARTIAL SEMET MODEL.
Crystal grow	pH: 8 Details: 100 MM TRIS, 150 MM NACL, 17% PEG 5K MME, 7.5% GLYCEROL, 1% PICOLINE, pH 8.00

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.771
Detector	Type: ADSC CCD / Detector: CCD / Date: May 5, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.771 Å / Relative weight: 1
Reflection	Resolution: 2.8→65 Å / Num. obs: 21257 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 11 % / B_iso Wilson estimate: 94.95 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 19.7
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 9.6 % / R_merge(I) obs: 0.94 / Mean I/σ(I) obs: 2.4 / % possible all: 77.4

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing
PHASER		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.8→115.47 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.91 / SU B: 38.096 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R: 1.817 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.295	1091	5.2 %	RANDOM
R_work	0.231	-	-	-
obs	0.234	20044	93.3 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 66.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.42 Å²	0 Å²	4.72 Å²
2-	-	3.52 Å²	0 Å²
3-	-	-	-5.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→115.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4839	0	0	6	4845

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	4925
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.535	1.958	6618
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.43	5	577
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.589	25.019	265
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.614	15	969
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.125	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	705
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3715
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.288	0.2	2839
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.325	0.2	3339
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	249
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	0.266	0.2	107
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.15	0.2	5
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	7.85	2	2980
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	12.232	4	4716
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	18.037	4	2165
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	24.916	8	1902
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

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	380	tight positional	0.12	0.1
2	B	264	tight positional	0.11	0.1
3	C	152	tight positional	0.09	0.1
1	A	433	medium positional	0.48	0.3
2	B	274	medium positional	0.53	0.3
3	C	90	medium positional	0.34	0.3
3	C	64	loose positional	1.4	5
1	A	380	tight thermal	3.11	5
2	B	264	tight thermal	2.92	5
3	C	152	tight thermal	2.34	5
1	A	433	medium thermal	7.13	10
2	B	274	medium thermal	6.89	10
3	C	90	medium thermal	5.91	10
3	C	64	loose thermal	5.87	10

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.648	65
R_work	0.476	1008

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	4.1641	-0.8302	-6.0102	0.824	0.5147	9.3844	0.0224	0.3644	-0.0258	-0.1401	-0.0555	-0.2269	-0.8508	0.3811	0.0331	0.0691	0.023	0.0722	0.2004	-0.0788	-0.1006	20.7448	25.4268	-69.2925
2	2.8402	2.3967	-3.3447	3.7442	-4.005	6.1734	0.0082	-0.3533	-0.0661	-0.169	-0.3061	-0.1302	0.0885	0.9079	0.2979	-0.1447	0.1678	-0.011	-0.2383	-0.0147	-0.339	6.0057	9.2942	-30.1042
3	4.6874	7.0863	-4.8354	15.8826	-6.7107	5.269	-0.0296	-0.2801	-0.5246	0.1021	-0.1566	-0.3359	0.0354	0.2538	0.1863	-0.3464	0.14	-0.0349	0.098	0.0851	-0.0749	-18.7418	-25.9097	3.5102
4	3.9823	0.3737	-4.7501	0.805	1.7957	12.1914	-0.4416	-0.6576	-0.4963	0.5155	0.1466	0.1215	0.7251	-0.2723	0.295	-0.1949	0.125	0.0889	0.0199	0.0179	-0.0398	-23.7613	13.0323	20.8774
5	1.3434	0.4946	-2.1175	3.5011	-3.0886	6.278	0.2806	-0.1959	0.1352	-0.1744	-0.1747	-0.2569	-0.8604	0.7068	-0.1059	-0.2078	-0.2507	0.027	-0.2935	-0.1747	-0.2802	-1.6777	28.723	-14.7337
6	0.2902	-0.0056	-1.2449	12.4178	-5.84	8.1094	0.2578	0.0468	0.1109	0.088	-0.6789	0.2126	-0.4595	0.6039	0.4211	0.1428	-0.2104	-0.0632	0.2841	0.0628	0.0408	9.8594	64.1021	-54.6997

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	81 - 101
2	X-RAY DIFFRACTION	1	C	9 - 57
3	X-RAY DIFFRACTION	2	A	42 - 80
4	X-RAY DIFFRACTION	2	B	24 - 95
5	X-RAY DIFFRACTION	2	B	4 - 19
6	X-RAY DIFFRACTION	2	C	58 - 69
7	X-RAY DIFFRACTION	3	A	1 - 41
8	X-RAY DIFFRACTION	3	B	96 - 122
9	X-RAY DIFFRACTION	4	D	81 - 101
10	X-RAY DIFFRACTION	4	F	9 - 57
11	X-RAY DIFFRACTION	5	D	42 - 80
12	X-RAY DIFFRACTION	5	E	24 - 95
13	X-RAY DIFFRACTION	5	E	4 - 19
14	X-RAY DIFFRACTION	5	F	58 - 69
15	X-RAY DIFFRACTION	6	D	1 - 41
16	X-RAY DIFFRACTION	6	E	96 - 122

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