+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+79 | ||||||
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Title | Bovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide) | ||||||
Components | (ATP SYNTHASE ...) x 5 | ||||||
Keywords | HYDROLASE / ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / F1FO ATP SYNTHASE / CENTRAL STALK | ||||||
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: 2.4 Å | ||||||
Authors | Gibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: The Structure of the Central Stalk in Bovine F(1)-ATPase at 2.4 A Resolution. Authors: Gibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. #1: Journal: Science / Year: 1999 Title: Molecular Architecture of the Rotary Motor in ATP Synthase Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E. #2: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1998 Title: ATP Synthesis by Rotary Catalysis (Nobel Lecture) Authors: Walker, J.E. #3: Journal: Structure / Year: 1997 Title: Crystal Structure of the Epsilon Subunit of the Proton-Translocating ATP Synthase from Escherichia Coli Authors: Uhlin, U. / Cox, G.B. / Guss, J.M. #4: 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. #5: 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. #6: Journal: J.Biol.Chem. / Year: 1981 Title: Inactivation of Bovine Mitochondrial F1-ATPase with Dicyclohexyl-Carbodiimide [14C] Leads to the Modification of a Specific Glutamic-Acid Residue in the Beta Subunit Authors: Esch, F.S. / Bohlen, P. / Otsuka, A.S. / Yoshida, M. / Allison, W.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e79.cif.gz | 651 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e79.ent.gz | 527.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/1e79 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/1e79 | 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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-Components
-ATP SYNTHASE ... , 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 / Organelle: MITOCHONDRION / Tissue: MUSCLESkeletal muscle / References: UniProt: P19483, EC: 3.6.1.34 #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLESkeletal muscle / References: UniProt: P00829, EC: 3.6.1.34 #3: Protein | | Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLESkeletal muscle / References: UniProt: P05631, EC: 3.6.1.34 #4: Protein | | Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLESkeletal muscle / References: UniProt: P05630, EC: 3.6.1.34 #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 / Organelle: MITOCHONDRION / Tissue: MUSCLESkeletal muscle / References: UniProt: P05632, EC: 3.6.1.34 |
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-Non-polymers , 7 types, 924 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | #9: Chemical | ChemComp-GOL / | #10: Chemical | ChemComp-DCW / | #11: Chemical | ChemComp-SO4 / | #12: Water | ChemComp-HOH / | |
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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 REFERENCE 4 , 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: 2.61 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / 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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 23, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 140093 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 36.405 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.1 / % possible all: 68.6 |
Reflection shell | *PLUS % possible obs: 68.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB CODE 1E1Q, NATIVE FROZEN BOVINE MITOCHONDRIAL F1-ATPASE Resolution: 2.4→20 Å / SU B: 10.4 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.31 Details: INITIAL REFINEMENT CARRIED OUT WITH REFMAC AND CNS UNRESOLVED SECTIONS ARE THE N-TERMINAL REGIONS OF THE ALPHA- AND BETA-SUBUNITS (RESIDUES 1-18 AND -4 - 8, RESPECTIVELY), THE C-TERMINAL ...Details: INITIAL REFINEMENT CARRIED OUT WITH REFMAC AND CNS UNRESOLVED SECTIONS ARE THE N-TERMINAL REGIONS OF THE ALPHA- AND BETA-SUBUNITS (RESIDUES 1-18 AND -4 - 8, RESPECTIVELY), THE C-TERMINAL REGIONS OF THE BETA-SUBUNITS (RESIDUES 475-478 IN TWO BETA-SUBUNITS AND 476-478 IN THE THIRD), TWO LOOP REGIONS IN THE GAMMA-SUBUNIT (RESIDUES 62-66 AND 97-100), RESIDUES 1-14 AND THE C-TERMINAL RESIDUE (146) OF THE DELTA-SUBUNIT, AND 3 RESIDUES (48-50) AT THE C-TERMINUS OF THE EPSILON-SUBUNIT. ASP 270 IN CHAINS A, B, C AND THE PEPTIDE BOND BETWEEN ASP 256 AND ASN 257 IN CHAINS D, E, AND F HAVE BEEN MODELED IN A CIS CONFORMATION. RESIDUAL FEATURES IN THE ELECTRON DENSITY MAP SUGGEST THAT THERE IS SOME CONFORMATIONAL DISORDER IN ASP 270 IN CHAINS A, B, AND C. REVDAT 2 INVOLVED RESIDUES 53-61 OF THE GAMMA SUBUNIT WHERE AN OUT-OF-REGISTER ERROR WAS CORRECTED
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Displacement parameters | Biso mean: 58.084 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 58.084 Å2 |