+Open data
-Basic information
Entry | Database: PDB / ID: 2f43 | ||||||
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Title | Rat liver F1-ATPase | ||||||
Components | (ATP synthase ...) x 3 | ||||||
Keywords | HYDROLASE / ATP SYNTHASE / F0F1-ATPASE / OXIDATIVE PHOSPHORYLATION / MITOCHONDRIA / VANADATE | ||||||
Function / homology | Function and homology information 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 / ATP biosynthetic process ...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 / ATP biosynthetic process / angiostatin binding / cellular response to peptide / 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-transporting ATPase activity, rotational mechanism / proton transmembrane transport / 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 / protease binding / angiogenesis / response to ethanol / mitochondrial inner membrane / membrane raft / calcium ion binding / cell surface / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Chen, C. / Saxena, A.K. / Simcoke, W.N. / Garboczi, D.N. / Pedersen, P.L. / Ko, Y.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Mitochondrial ATP synthase: Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism. Authors: Chen, C. / Saxena, A.K. / Simcoke, W.N. / Garboczi, D.N. / Pedersen, P.L. / Ko, Y.H. #1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1998 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. #2: Journal: Biochim.Biophys.Acta / Year: 1994 Title: The three-dimensional structure of rat liver mitochodria F1-ATPase: X-ray diffraction studies. Authors: Bianchet, M. / Medjahed, D. / Hulihen, J. / Pedersen, P.L. / Amzel, L.M. #3: Journal: J.Bioenerg.Biomembr. / Year: 1992 Title: Quaternary structure of ATP synthases: symmetry and asymmetry in the F1 moiety. Authors: Amzel, L.M. / Bianchet, M.A. / Pedersen, P.L. #4: Journal: J.Biol.Chem. / Year: 1991 Title: Mitochondrial ATP synthase. Quaternary structure of the F1 moiety at 3.6 A determined by x-ray diffraction analysis. Authors: Bianchet, M. / Ysern, X. / Hullihen, J. / Pedersen, P.L. / Amzel, L.M. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THIS PROTEIN HAS AN UNUSUAL STOICHIOMETRY AND THUS, UNUSUAL SYMMETRY. THE BIOLOGICAL UNIT (ACTIVE ENZYME) IS COMPOSED OF 3 A CHAINS, 3 B CHAINS AND 1 G CHAIN. IN THE R32 SPACEGROUP OF THIS CRYSTAL, THE ASYMMETRIC UNIT IS MADE UP OF ONE A CHAIN, ONE B CHAIN AND ONE-THIRD OF A G CHAIN. THE G CHAIN LIES ON THE 3-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS AND EACH ASYMMETRIC UNIT CONTAINS A RANDOM ONE OF THE THREE CRYSTALLOGRAPHICALLY SYMMETRIC POSITIONS. TO MAKE A BIOMOLECULE, THE 3-FOLD MATRICES IN REMARK 350 ARE ONLY APPLIED TO CHAIN A AND CHAIN B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f43.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f43.ent.gz | 172.4 KB | Display | PDB format |
PDBx/mmJSON format | 2f43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/2f43 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f43 | HTTPS FTP |
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-Related structure data
Related structure data | 1mabS 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 ... , 3 types, 3 molecules ABG
#1: Protein | Mass: 55334.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER References: UniProt: P15999, H+-transporting two-sector ATPase |
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#2: Protein | Mass: 51404.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER References: UniProt: P10719, H+-transporting two-sector ATPase |
#3: Protein | Mass: 30231.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER References: UniProt: P35435, H+-transporting two-sector ATPase |
-Non-polymers , 4 types, 5 molecules
#4: Chemical | #5: Chemical | ChemComp-ATP / | #6: Chemical | ChemComp-VO4 / | #7: Chemical | ChemComp-ADP / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 296 K / pH: 8.08 Details: 5MM ATP, 5MM MGCL2, 5MM VANADATE, 25MM NAN3, 50MM MOPS, pH 8.08, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99092 |
Detector | Type: SBC-2 / Detector: CCD / Details: MONOCROMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99092 Å / Relative weight: 1 |
Reflection | Resolution: 3→73.52 Å / Num. obs: 29647 / % possible obs: 100 % / Redundancy: 8.7 % / Rsym value: 0.143 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.75 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MAB Resolution: 3→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 7286337.69 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.4837 Å2 / ksol: 0.277358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Total num. of bins used: 10
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