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Yorodumi- PDB-7tgv: Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tgv | |||||||||||||||||||||
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Title | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B2 | |||||||||||||||||||||
Components | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | |||||||||||||||||||||
Keywords | ISOMERASE/ISOMERASE inhibitor / Peptidyl-prolyl isomerase / oxidative stress / necrosis / mitochondrial permeability / ISOMERASE / ISOMERASE-ISOMERASE inhibitor complex | |||||||||||||||||||||
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) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 | 7tgv.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tgv.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 7tgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/7tgv ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tgv | HTTPS FTP |
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-Related structure data
Related structure data | 7tgsC 7tgtC 7tguC 7th1C 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: 17652.125 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) / References: UniProt: P30405, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-I3X / ( |
#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: 2.44 Å3/Da / Density % sol: 49.6 % / 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: 1.46→37.7 Å / Num. obs: 31004 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 9.55 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.06 / Rrim(I) all: 0.131 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.46→1.486 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1557 / CC1/2: 0.574 / CC star: 0.91 / Rpim(I) all: 0.507 / Rrim(I) all: 1.167 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BIT Resolution: 1.46→37.7 Å / SU ML: 0.1032 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.6986 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: 12.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→37.7 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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