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Open data
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Basic information
Entry | Database: PDB / ID: 1mab | ||||||
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Title | RAT LIVER F1-ATPASE | ||||||
![]() | (PROTEIN (F1-ATPASE ...) x 3 | ||||||
![]() | HYDROLASE / ATP SYNTHASE / FOF1-ATPASE / OXIDATIVE PHOSPHORYLATION / MITOCHONDRIA | ||||||
Function / homology | ![]() lipoprotein particle receptor activity / Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / negative regulation of cell adhesion involved in substrate-bound cell migration / response to curcumin / response to 3,3',5-triiodo-L-thyronine / cold acclimation / cellular response to peptide ...lipoprotein particle receptor activity / Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / negative regulation of cell adhesion involved in substrate-bound cell migration / response to curcumin / response to 3,3',5-triiodo-L-thyronine / cold acclimation / cellular response to peptide / ATP biosynthetic process / angiostatin binding / COP9 signalosome / proton-transporting ATP synthase complex / cellular response to interleukin-7 / response to muscle activity / response to manganese ion / : / : / mitochondrial nucleoid / : / MHC class I protein binding / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / cellular response to nitric oxide / positive regulation of blood vessel endothelial cell migration / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / cellular response to dexamethasone stimulus / receptor-mediated endocytosis / liver development / mitochondrial membrane / regulation of intracellular pH / lipid metabolic process / ADP binding / angiogenesis / response to ethanol / protease binding / mitochondrial inner membrane / membrane raft / calcium ion binding / cell surface / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bianchet, M.A. / Amzel, L.M. | ||||||
![]() | ![]() Title: The 2.8-A structure of rat liver F1-ATPase: configuration of a critical intermediate in ATP synthesis/hydrolysis. Authors: Bianchet, M.A. / Hullihen, J. / Pedersen, P.L. / Amzel, L.M. #1: ![]() Title: The Three-Dimensional Structure of Rat Liver Mitochondria F1-ATPase: X-Ray Diffraction Studies Authors: Bianchet, M.A. / Medjahed, D. / Hullihen, J. / Pedersen, P.L. / Amzel, L.M. #2: ![]() Title: Quaternary Structure of ATP Synthases: Symmetry and Asymmetry in the F1 Moiety Authors: Amzel, L.M. / Bianchet, M.A. / Pedersen, P.L. #3: ![]() Title: Quaternary Structure of ATP Synthases: Symmetry and Asymmetry in the F1 Moiety Authors: Bianchet, M.A. / Ysernhullihen, J. / Pedersen, P.L. / Amzel, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.3 KB | Display | ![]() |
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PDB format | ![]() | 176.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 552.7 KB | Display | ![]() |
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Full document | ![]() | 637.1 KB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 50.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-PROTEIN (F1-ATPASE ... , 3 types, 3 molecules ABG
#1: Protein | Mass: 55348.219 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 51404.461 Da / Num. of mol.: 1 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 29974.396 Da / Num. of mol.: 1 / Fragment: GAMMA CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 5 types, 65 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-ATP / |
#6: Chemical | ChemComp-PO4 / |
#7: Chemical | ChemComp-ADP / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.14 Details: 2.1 M AMMONIUM SULFATE AS PRECIPITANT, 0.2 M KPI (PH 7.14) BUFFER, 0.005 M ATP. AT ROOM TEMPERATURE Temp details: room temp | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.45 / Method: microdialysis / Details: Amzel, L.M., (1978) J.Biol.Chem., 253, 2067. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Details: MONOCROMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 35334 / % possible obs: 85.3 % / Redundancy: 11 % / Rsym value: 0.103 / Net I/σ(I): 7.1 |
Reflection | *PLUS Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS Mean I/σ(I) obs: 7.1 |
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Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Details: FURTHER REFINEMENT IS IN PROGRESS. BECAUSE OF THE CRYSTAL SYMMETRY, THE INTERPRETABLE REGIONS OF THE GAMMA SUBUNIT ARE SEEN AS PARTIALLY OCCUPIED OVERLAPING COPIES. GAMMA AND SMALL REGIONS ...Details: FURTHER REFINEMENT IS IN PROGRESS. BECAUSE OF THE CRYSTAL SYMMETRY, THE INTERPRETABLE REGIONS OF THE GAMMA SUBUNIT ARE SEEN AS PARTIALLY OCCUPIED OVERLAPING COPIES. GAMMA AND SMALL REGIONS OF ALPHA AND BETA-SUBUNIT INTERACTING WITH GAMMA ARE REFINED WITH A PARTIAL OCUPPANCY.
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Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 6 Å / σ(F): 3 / % reflection Rfree: 2.5 % / Rfactor Rfree: 0.29 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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