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

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Basic information

Entry
Database: PDB / ID: 2cly
TitleSubcomplex 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
KeywordsHYDROLASE / 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 protein degradation / proton-transporting ATP synthase complex / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / : / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #200 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2210 / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #200 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2210 / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKane 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: The Expression, Purification, Crystallization and Preliminary X-Ray Analysis of a Subcomplex of the Peripheral Stalk of ATP Synthase from Bovine Mitochondria
Authors: Silvester, J.A. / Kane Dickson, V. / Runswick, M.J. / Leslie, A.G.W. / Walker, J.E.
History
DepositionMay 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: 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
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,8186
Polymers104,8186
Non-polymers00
Water1086
1
A: ATP SYNTHASE B CHAIN, MITOCHONDRIAL
B: ATP SYNTHASE D CHAIN, MITOCHONDRIAL
C: ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)52,4093
Polymers52,4093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: ATP SYNTHASE B CHAIN, MITOCHONDRIAL
E: ATP SYNTHASE D CHAIN, MITOCHONDRIAL
F: ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)52,4093
Polymers52,4093
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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 number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A5 - 56
2112D5 - 56
1212A57 - 99
2212D57 - 99
1122B19 - 39
2122E19 - 39
1222B44 - 49
2222E44 - 49
1322B78 - 99
2322E78 - 99
1422B106 - 122
2422E106 - 122
1132C37 - 56
2132F37 - 56
1233C18 - 35
2233F18 - 35

NCS ensembles :
ID
1
2
3

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Components

#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 (domestic 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 (domestic 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 (domestic 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


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 79-183 ONLY NO PRESEQUENCE, RESIDUES 5-70 NO INITIATOR METHIONINE, RESIDUES 3-123

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity 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 growpH: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.771
DetectorType: ADSC CCD / Detector: CCD / Date: May 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.8→65 Å / Num. obs: 21257 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 94.95 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.4 / % possible all: 77.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
PHASERphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→115.47 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1091 5.2 %RANDOM
Rwork0.231 ---
obs0.234 20044 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å24.72 Å2
2--3.52 Å20 Å2
3----5.44 Å2
Refinement stepCycle: LAST / Resolution: 2.8→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 0 0 6 4845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224925
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9586618
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58925.019265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.61415969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1251535
X-RAY DIFFRACTIONr_chiral_restr0.1120.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023715
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2880.22839
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.23339
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.2107
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.8522980
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.23244716
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it18.03742165
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it24.91681902
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A380tight positional0.120.1
2B264tight positional0.110.1
3C152tight positional0.090.1
1A433medium positional0.480.3
2B274medium positional0.530.3
3C90medium positional0.340.3
3C64loose positional1.45
1A380tight thermal3.115
2B264tight thermal2.925
3C152tight thermal2.345
1A433medium thermal7.1310
2B274medium thermal6.8910
3C90medium thermal5.9110
3C64loose thermal5.8710
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.648 65
Rwork0.476 1008
Refinement TLS params.

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

IDL11 (°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)
14.1641-0.8302-6.01020.8240.51479.38440.02240.3644-0.0258-0.1401-0.0555-0.2269-0.85080.38110.03310.06910.0230.07220.2004-0.0788-0.100620.744825.4268-69.2925
22.84022.3967-3.34473.7442-4.0056.17340.0082-0.3533-0.0661-0.169-0.3061-0.13020.08850.90790.2979-0.14470.1678-0.011-0.2383-0.0147-0.3396.00579.2942-30.1042
34.68747.0863-4.835415.8826-6.71075.269-0.0296-0.2801-0.52460.1021-0.1566-0.33590.03540.25380.1863-0.34640.14-0.03490.0980.0851-0.0749-18.7418-25.90973.5102
43.98230.3737-4.75010.8051.795712.1914-0.4416-0.6576-0.49630.51550.14660.12150.7251-0.27230.295-0.19490.1250.08890.01990.0179-0.0398-23.761313.032320.8774
51.34340.4946-2.11753.5011-3.08866.2780.2806-0.19590.1352-0.1744-0.1747-0.2569-0.86040.7068-0.1059-0.2078-0.25070.027-0.2935-0.1747-0.2802-1.677728.723-14.7337
60.2902-0.0056-1.244912.4178-5.848.10940.25780.04680.11090.088-0.67890.2126-0.45950.60390.42110.1428-0.2104-0.06320.28410.06280.04089.859464.1021-54.6997
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A81 - 101
2X-RAY DIFFRACTION1C9 - 57
3X-RAY DIFFRACTION2A42 - 80
4X-RAY DIFFRACTION2B24 - 95
5X-RAY DIFFRACTION2B4 - 19
6X-RAY DIFFRACTION2C58 - 69
7X-RAY DIFFRACTION3A1 - 41
8X-RAY DIFFRACTION3B96 - 122
9X-RAY DIFFRACTION4D81 - 101
10X-RAY DIFFRACTION4F9 - 57
11X-RAY DIFFRACTION5D42 - 80
12X-RAY DIFFRACTION5E24 - 95
13X-RAY DIFFRACTION5E4 - 19
14X-RAY DIFFRACTION5F58 - 69
15X-RAY DIFFRACTION6D1 - 41
16X-RAY DIFFRACTION6E96 - 122

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