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Yorodumi- PDB-4asu: F1-ATPase in which all three catalytic sites contain bound nucleo... -
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-Basic information
Entry | Database: PDB / ID: 4asu | ||||||
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Title | F1-ATPase in which all three catalytic sites contain bound nucleotide, with magnesium ion released in the Empty site | ||||||
Components | (ATP SYNTHASE SUBUNIT ...) x 5 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / mitochondrial proton-transporting ATP synthase, catalytic core / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / mitochondrial proton-transporting ATP synthase, catalytic core / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / aerobic respiration / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Rees, D.M. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural Evidence of a New Catalytic Intermediate in the Pathway of ATP Hydrolysis by F1-ATPase from Bovine Heart Mitochondria. Authors: Rees, D.M. / Montgomery, M.G. / Leslie, A.G. / 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 19-STRANDED BARREL THIS IS REPRESENTED BY A 20-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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4asu.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4asu.ent.gz | 988.4 KB | Display | PDB format |
PDBx/mmJSON format | 4asu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/4asu ftp://data.pdbj.org/pub/pdb/validation_reports/as/4asu | HTTPS FTP |
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-Related structure data
Related structure data | 2jdiS 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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-Components
-ATP SYNTHASE SUBUNIT ... , 5 types, 9 molecules ABCDEFGHI
#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: 51615.684 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: 30300.760 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 #4: Protein | | Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P05630 #5: Protein/peptide | | Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P05632 |
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-Non-polymers , 3 types, 319 molecules
#6: Chemical | ChemComp-ADP / #7: Chemical | ChemComp-MG / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | DIFFERENT RESIDUE: GLY A 481, GLY B 481, GLY C 481 THIS RESIDUE WAS IDENTIFIED AS A GLY FROM THE ...DIFFERENT RESIDUE: GLY A 481, GLY B 481, GLY C 481 THIS RESIDUE WAS IDENTIFIED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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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: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 2, 2006 / Details: TORODIAL FOCUSING MIRROR |
Radiation | Monochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→133.18 Å / Num. obs: 92081 / % possible obs: 78.4 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.59→2.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.7 / % possible all: 66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JDI Resolution: 2.6→63.5 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.864 / SU B: 31.727 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→63.5 Å
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Refine LS restraints |
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