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Yorodumi- PDB-5a0e: Crystal structure of cyclophilin D in complex with CsA analogue, JW47. -
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-Basic information
Entry | Database: PDB / ID: 5a0e | ||||||
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Title | Crystal structure of cyclophilin D in complex with CsA analogue, JW47. | ||||||
Components |
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Keywords | ISOMERASE / CYCLOPHILIN D / CYP D / PPIF / CYCLOSPORIN A / CSA / JW47 / MITOCHONDRIAL PERMEABILITY TRANSITION PORE / PTP / PEPTIDYLPROLYL CIS-TRANS ISOMERASE / CYCLOPHILIN | ||||||
Function / homology | Function and homology information regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / necroptotic process / negative regulation of intrinsic apoptotic signaling pathway / protein peptidyl-prolyl isomerization / cellular response to calcium ion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to ischemia / cellular response to hydrogen peroxide / protein folding / mitochondrial inner membrane / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) CYLINDROCARPON LUCIDUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Warne, J. / Pryce, G. / Hill, J. / Shi, X. / Lenneras, F. / Puentes, F. / Kip, M. / Hilditch, L. / Walker, P. / Simone, M. ...Warne, J. / Pryce, G. / Hill, J. / Shi, X. / Lenneras, F. / Puentes, F. / Kip, M. / Hilditch, L. / Walker, P. / Simone, M. / Chan, A.W.E. / Towers, G. / Coker, A.R. / Duchen, M. / Szabadkai, G. / Baker, D. / Selwood, D.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Selective Inhibition of the Mitochondrial Permeability Transition Pore Protects Against Neuro-Degeneration in Experimental Multiple Sclerosis. Authors: Warne, J. / Pryce, G. / Hill, J. / Shi, X. / Lenneras, F. / Puentes, F. / Kip, M. / Hilditch, L. / Walker, P. / Simone, M.I. / Chan, A.W.E. / Towers, G.J. / Coker, A.R. / Duchen, M.R. / ...Authors: Warne, J. / Pryce, G. / Hill, J. / Shi, X. / Lenneras, F. / Puentes, F. / Kip, M. / Hilditch, L. / Walker, P. / Simone, M.I. / Chan, A.W.E. / Towers, G.J. / Coker, A.R. / Duchen, M.R. / Szabadkai, G. / Baker, D. / Selwood, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a0e.cif.gz | 160.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a0e.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 5a0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0e ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0e | HTTPS FTP |
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-Related structure data
Related structure data | 2z6wS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17739.205 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P30405, peptidylprolyl isomerase #2: Protein/peptide | Mass: 1376.829 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CYCLOSPORINE A WITH 1-(PENT-4-ENYL) QUINOLINIUM LINKED TO THE BMT RESIDUE. Source: (synth.) CYLINDROCARPON LUCIDUM (fungus) #3: Water | ChemComp-HOH / | Nonpolymer details | 4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE (BMT): 1-PENT-4-ENYL QUINOLINIUM LINKED TO CH OF ...4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE (BMT): 1-PENT-4-ENYL QUINOLINIU | Sequence details | K133I MUTATION | |
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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: 2.04 Å3/Da / Density % sol: 39.6 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 2.9 Details: HANGING DROP 50:50. PRECIPITANT: 23% POLYETHYLENE GLYCOL (PEG3350), 50 MM SODIUM-CITRATE BUFFER AT PH 2.9 PROTEIN: 30 MG/ML IN 50MM POTASSIUM/SODIUM PHOSPHATE PH 7.3, 100MM NACL, 2MM EDTA, 0.02% SODIUM AZIDE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9174 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2015 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→35.99 Å / Num. obs: 101898 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.12→1.15 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.8 / % possible all: 45.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z6W Resolution: 1.25→35.99 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.994 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→35.99 Å
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Refine LS restraints |
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