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Yorodumi- PDB-2v7q: The structure of F1-ATPase inhibited by I1-60HIS, a monomeric for... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v7q | ||||||
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Title | The structure of F1-ATPase inhibited by I1-60HIS, a monomeric form of the inhibitor protein, IF1. | ||||||
Components |
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Keywords | HYDROLASE / ION TRANSPORT / MITOCHONDRION / TRANSIT PEPTIDE / INHIBITOR PROTEIN | ||||||
Function / homology | Function and homology information angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / proton-transporting ATP synthase complex / heme biosynthetic process / : ...angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / proton-transporting ATP synthase complex / heme biosynthetic process / : / : / Mitochondrial protein degradation / : / negative regulation of endothelial cell proliferation / 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 / erythrocyte differentiation / proton motive force-driven mitochondrial ATP synthesis / aerobic respiration / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: How the Regulatory Protein, If1, Inhibits F1- ATPase from Bovine Mitochondria. Authors: Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" 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 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7q.cif.gz | 679.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7q.ent.gz | 552.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v7q_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2v7q_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2v7q_validation.xml.gz | 92.7 KB | Display | |
Data in CIF | 2v7q_validation.cif.gz | 136.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7q ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7q | HTTPS FTP |
-Related structure data
Related structure data | 1ohhS 2uys 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: 55332.219 Da / Num. of mol.: 3 / Fragment: RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE References: UniProt: Q1JQC4, UniProt: P19483*PLUS, EC: 3.6.1.14 #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Fragment: RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.14 #3: Protein | | Mass: 30185.674 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-297 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34 #4: Protein | | Mass: 15074.813 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-168 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P05630, EC: 3.6.1.14 #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 / Tissue: MUSCLE / References: UniProt: P05632, EC: 3.6.1.14 |
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-Protein , 1 types, 1 molecules J
#6: Protein | Mass: 7462.098 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-85 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: MUSCLE / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01096 |
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-Non-polymers , 5 types, 1951 molecules
#7: Chemical | #8: Chemical | ChemComp-MG / #9: Chemical | #10: Chemical | ChemComp-PO4 / | #11: Water | ChemComp-HOH / | |
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-Details
Sequence details | I1-60HIS IS A TRUNCATED FRAGMENT OF THE BOVINE ATPASE INHIBITOR PROTEIN. RESIDUES 1-60 PLUS 6 C- ...I1-60HIS IS A TRUNCATED FRAGMENT OF THE BOVINE ATPASE INHIBITOR PROTEIN. RESIDUES 1-60 PLUS 6 C-TERMINAL HISTIDINES |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.21 % / Description: NONE |
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Crystal grow | pH: 8.2 / Details: pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→69.7 Å / Num. obs: 212416 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OHH Resolution: 2.1→37.19 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.233 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 41.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.19 Å
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Refine LS restraints |
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