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Yorodumi- PDB-1ohh: BOVINE MITOCHONDRIAL F1-ATPASE complexed with the inhibitor prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ohh | ||||||
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Title | BOVINE MITOCHONDRIAL F1-ATPASE complexed with the inhibitor protein IF1 | ||||||
Components |
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Keywords | SYNTHASE / ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE | ||||||
Function / homology | Function and homology information angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / negative regulation of hydrolase activity / mitochondrial proton-transporting ATP synthase, catalytic core / heme biosynthetic process / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / negative regulation of endothelial cell proliferation ...angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / negative regulation of hydrolase activity / mitochondrial proton-transporting ATP synthase, catalytic core / heme biosynthetic process / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / negative regulation of endothelial cell proliferation / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / structural molecule activity / cell surface / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Cabezon, E. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: The Structure of Bovine F1-ATPase in Complex with its Regulatory Protein If1 Authors: Cabezon, E. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. #1: Journal: Nature / Year: 1994 Title: Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria Authors: Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization of F1-ATPase from Bovine Heart Mitochondria Authors: Lutter, R. / Abrahams, J.P. / Van Raaij, M.J. / Todd, R.J. / Lundqvist, T. / Buchanan, S.K. / Leslie, A.G. / Walker, J.E. #3: Journal: Embo J. / Year: 1993 Title: The Structure of Bovine If1, the Regulatory Subunit of Mitochondrial F-ATPase Authors: Cabezon, E. / Runswick, M.J. / Leslie, A.G.W. / Walker, J.E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 17-STRANDED BARREL THIS IS REPRESENTED BY A 18-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ohh.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1ohh.ent.gz | 910.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ohh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1ohh ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1ohh | HTTPS FTP |
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-Related structure data
Related structure data | 1e1qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Number of models | 2 |
-Components
-ATP synthase subunit ... , 3 types, 7 molecules ABCDEFG
#1: Protein | Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P19483 #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle References: UniProt: P00829, H+-transporting two-sector ATPase #3: Protein | | Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P05631 |
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-Protein , 1 types, 1 molecules H
#4: Protein | Mass: 9604.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: MUSCLESkeletal muscle / Gene: ATPIF1, ATPI / Organ: HEART / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P01096 |
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-Non-polymers , 2 types, 10 molecules
#5: Chemical | ChemComp-ANP / #6: Chemical | ChemComp-MG / |
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-Details
Compound details | THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THE ...THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THE CATALYTIC BETA SUBUNIT. IN THE REFERENCE STRUCTURE, (REFERENCE 1) THE BETA SUBUNITS WERE LABELED ACCORDING TO THE BOUND NUCLEOTIDE |
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Sequence details | REFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, ...REFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, BIOCHEMIST |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.6 Details: PROTEIN 20MG/ML IN 100MM PIPES-NAOH PH6.6, 40MM MGSO4, 0.04% NA AZIDE, 10% GLYCEROL, 0.002% PMSF. DROPS EQUAL VOLUME OF PROTEIN AND 10MM AMP-PNP, 300MM NACL, 16% PEG 4000, 5MM SPERMIDINE. BATCH METHOD., pH 6.60 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9366 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9366 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→39.5 Å / Num. obs: 109367 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.03 % / Biso Wilson estimate: 82.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.61→2.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 7.1 / % possible all: 99.1 |
Reflection | *PLUS Highest resolution: 2.8 Å / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS % possible obs: 97.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 1E1Q, BOVINE MITOCHONDRIAL F1-ATPASE Resolution: 2.8→39.5 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: CRYSTALS ARE STATISTICALLY DISORDERED. IN THE ASYMMETRIC UNIT, THERE ARE TWO SUPERPOSED MOLECULES (COMPLEX A AND B) RELATED BY A 120 DEGREE ROTATION, EACH HAVE BEEN ASSIGNED AN OCCUPANCY OF ...Details: CRYSTALS ARE STATISTICALLY DISORDERED. IN THE ASYMMETRIC UNIT, THERE ARE TWO SUPERPOSED MOLECULES (COMPLEX A AND B) RELATED BY A 120 DEGREE ROTATION, EACH HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.5 AND THEY ARE TREATED AS ALTERNATIVE CONFORMATIONS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.8 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→39.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.82 Å / Total num. of bins used: 50
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Refinement | *PLUS Rfactor Rfree: 0.277 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.44 |