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Yorodumi- PDB-1h8e: (ADP.AlF4)2(ADP.SO4) bovine F1-ATPase (all three catalytic sites ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h8e | ||||||
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Title | (ADP.AlF4)2(ADP.SO4) bovine F1-ATPase (all three catalytic sites occupied) | ||||||
Components | (BOVINE MITOCHONDRIAL F1- ...) x 5 | ||||||
Keywords | HYDROLASE / ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE | ||||||
Function / homology | Function and homology information Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / : / proton transmembrane transporter activity ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / 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 / proton motive force-driven mitochondrial ATP synthesis / aerobic respiration / 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 Å | ||||||
Authors | Menz, R.I. / Walker, J.E. / Leslie, A.G.W. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2001 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. #1: Journal: Nat.Struct.Biol. / Year: 2000 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. #2: Journal: Science / Year: 1999 Title: Molecular Architecture of the Rotary Motor in ATP Synthase Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E. #3: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1998 Title: ATP Synthesis by Rotary Catalysis (Nobel Lecture) Authors: Walker, J.E. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h8e.cif.gz | 656.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8e.ent.gz | 530.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h8e_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 1h8e_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 1h8e_validation.xml.gz | 134.8 KB | Display | |
Data in CIF | 1h8e_validation.cif.gz | 191.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8e ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8e | HTTPS FTP |
-Related structure data
Related structure data | 1bmfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTICALPHA SUBUNIT AND THREE COPIES OF THE CATALYTIC BETA SUBUNIT.IN THE 1994 REFERENCE, THE BETA SUBUNITS WERE LABELED ACCORDINGTO THE BOUND NUCLEOTIDE, ASBETA(DP) (BINDS ADP),BETA(E) (NO BOUND NUCLEOTIDE) ANDBETA(TP ) (AMPPNP BOUND).THE ALPHA SUBUNITS (WHICH ALL BIND AMPPNP) CONTRIBUTE TO THECATALYTIC SITES OF THE BETA SUBUNITS, AND HAVE BEEN LABELEDACCORDINGLY . THUSALPHA(DP) CONTRIBUTES TO THE CATALYTIC SITE ON BETA(DP),ALPHA(TP) TO THE SITE ON BETA ( TP) ANDALPHA(E) TO THE SITE ON BETA(E).THE CORRESPONDENCE BETWEEN THE SUBUNIT NAMES AND THE CHAINIDENTIFIERS IS GIVEN BELOW:.CHAIN A: ALPHA(E )CHAIN B: ALPHA(TP)CHAIN C: ALPHA(DP)CHAIN D : BETA(DP)CHAIN E: BETA(E)CHAIN F: BETA(TP) CHAIN G: GAMMA SUBUNITCHAIN H: DELTA SUBUNITCHAIN I: EPSILON SUBUNIT |
-Components
-BOVINE MITOCHONDRIAL F1- ... , 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: 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: 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: 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: 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: MUSCLE / References: UniProt: P05632, EC: 3.6.1.34 |
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-Non-polymers , 6 types, 1712 molecules
#6: Chemical | ChemComp-ADP / #7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-GOL / #9: Chemical | #10: Chemical | ChemComp-SO4 / | #11: Water | ChemComp-HOH / | |
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-Details
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 |
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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: 2.64 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE., pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22-24 ℃ / pH: 7.2 / Method: microdialysis / Details: Lutter, R., (1993) J.Mol.Biol., 229, 787. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Aug 15, 1998 |
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→13.5 Å / Num. obs: 209953 / % possible obs: 79.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2→2.14 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.7 / % possible all: 40.6 |
Reflection shell | *PLUS % possible obs: 40.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB CODE 1BMF, NATIVE BOVINE MITOCHONDRIAL F1- ATPASE Resolution: 2→13.5 Å / SU B: 5.8 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.21 Details: INITIAL REFINEMENT CARRIED OUT WITH TNT. 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.
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Displacement parameters | Biso mean: 45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→13.5 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |