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Yorodumi- PDB-7th1: Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7th1 | |||||||||||||||||||||
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Title | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B3 | |||||||||||||||||||||
Components | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | |||||||||||||||||||||
Keywords | ISOMERASE / oxidative stress / necrosis / mitochondrial permeability | |||||||||||||||||||||
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 / negative regulation of ATP-dependent activity / cellular response to arsenic-containing substance / mitochondrial depolarization / 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 / negative regulation of ATP-dependent activity / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / necroptotic process / apoptotic mitochondrial changes / protein peptidyl-prolyl isomerization / negative regulation of intrinsic apoptotic signaling pathway / cellular response to calcium ion / peptidylprolyl isomerase / response to ischemia / peptidyl-prolyl cis-trans isomerase activity / peptide binding / 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) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | |||||||||||||||||||||
Authors | Rangwala, A.M. / Thakur, M.K. / Seeliger, M.A. / Peterson, A.A. / Liu, D.R. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Discovery and molecular basis of subtype-selective cyclophilin inhibitors. Authors: Peterson, A.A. / Rangwala, A.M. / Thakur, M.K. / Ward, P.S. / Hung, C. / Outhwaite, I.R. / Chan, A.I. / Usanov, D.L. / Mootha, V.K. / Seeliger, M.A. / Liu, D.R. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7th1.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7th1.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 7th1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7th1_validation.pdf.gz | 694.3 KB | Display | wwPDB validaton report |
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Full document | 7th1_full_validation.pdf.gz | 696.9 KB | Display | |
Data in XML | 7th1_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 7th1_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/7th1 ftp://data.pdbj.org/pub/pdb/validation_reports/th/7th1 | HTTPS FTP |
-Related structure data
Related structure data | 7tgsC 7tgtC 7tguC 7tgvC 7th6C 7th7C 7thcC 7thdC 7thfC 2bitS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17780.256 Da / Num. of mol.: 1 / Mutation: K175I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30405, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-I5J / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.9 % / Description: Bladed, tabular, roughly 0.3-0.5 mm in length |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 28% PEG 3350 0.5 M KH2PO4 Protein and inhibitor were mixed in ratio 1:3 1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2019 |
Radiation | Monochromator: Double Crystal Monochromator; Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→44.684 Å / Num. obs: 25507 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 13.97 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.05 / Rrim(I) all: 0.173 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.52→1.549 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.607 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1301 / CC1/2: 0.911 / CC star: 0.98 / Rpim(I) all: 0.456 / Rrim(I) all: 1.671 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BIT Resolution: 1.52→44.68 Å / SU ML: 0.1306 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8384 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→44.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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