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Open data
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Basic information
Entry | Database: PDB / ID: 1w0k | ||||||
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Title | ADP inhibited bovine F1-ATPase | ||||||
![]() | (ATP SYNTHASE ...) x 3 | ||||||
![]() | HYDROLASE / ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE / ATP SYNTHESIS / ATP-BINDING | ||||||
Function / homology | ![]() Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / Mitochondrial protein degradation / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / Mitochondrial protein degradation / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial 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 / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kagawa, R. / Montgomery, M.G. / Braig, K. / Walker, J.E. / Leslie, A.G.W. | ||||||
![]() | ![]() Title: The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride Authors: Kagawa, R. / Montgomery, M.G. / Braig, K. / Leslie, A.G.W. / Walker, J.E. #1: ![]() Title: Structure of Bovine Mitochondrial F1-ATPase with Nucleotide Bound to All Three Catalytic Sites; Implications for the Mechanism of Rotary Catalysis Authors: Menz, R.I. / Walker, J.E. / Leslie, A.G.W. #2: ![]() Title: The Structure of the Central Stalk in Bovine F1-ATPase at 2.4A Resolution Authors: Gibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. #3: ![]() Title: Molecular Architecture of the Rotary Motor in ATP Synthase Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E. #4: ![]() Title: ATP Synthesis by Rotary Catalysis (Nobel Lecture) Authors: Walker, J.E. #5: ![]() 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. #6: 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. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 569.3 KB | Display | ![]() |
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PDB format | ![]() | 461.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 103.5 KB | Display | |
Data in CIF | ![]() | 140.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w0jC ![]() 1bmfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-ATP SYNTHASE ... , 3 types, 7 molecules ABCDEFG
#1: Protein | Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P19483, H+-transporting two-sector ATPase #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() 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) ![]() ![]() References: UniProt: P05631, H+-transporting two-sector ATPase |
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-Non-polymers , 5 types, 280 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: 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 THE 1994 REFERENCE, 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, BIOCHEMISTRY ...REFERENCE: 1) FOR THE ALPHA SUBUNIT: J.E.WALKER, S.J.POWELL, O.VINAS AND M.J.RUNSWICK, BIOCHEMIST |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 54 % |
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Crystal grow | pH: 8.2 Details: CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE., pH 8.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 21, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→25.4 Å / Num. obs: 93001 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 6.1 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB CODE 1BMF, NATIVE BOVINE MITOCHONDRIAL F1- ATPASE Resolution: 2.85→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→20 Å
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Refine LS restraints |
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