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Yorodumi- PDB-3ici: Crystal structure of cyclophilin B in complex with calmegin fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ici | ||||||
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Title | Crystal structure of cyclophilin B in complex with calmegin fragment | ||||||
Components |
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Keywords | ISOMERASE / protein-protein complex / Endoplasmic reticulum / Glycoprotein / Rotamase / Chaperone / Lectin / Membrane / Phosphoprotein / Transmembrane | ||||||
Function / homology | Function and homology information positive regulation by host of viral genome replication / endoplasmic reticulum chaperone complex / Collagen biosynthesis and modifying enzymes / positive regulation by host of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / smooth endoplasmic reticulum / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding ...positive regulation by host of viral genome replication / endoplasmic reticulum chaperone complex / Collagen biosynthesis and modifying enzymes / positive regulation by host of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / smooth endoplasmic reticulum / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding / : / neutrophil chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / bone development / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / melanosome / protein folding / protein stabilization / endoplasmic reticulum lumen / focal adhesion / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kozlov, G. / Gehring, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural Basis of Cyclophilin B Binding by the Calnexin/Calreticulin P-domain. Authors: Kozlov, G. / Bastos-Aristizabal, S. / Maattanen, P. / Rosenauer, A. / Zheng, F. / Killikelly, A. / Trempe, J.F. / Thomas, D.Y. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ici.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ici.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ici.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/3ici ftp://data.pdbj.org/pub/pdb/validation_reports/ic/3ici | HTTPS FTP |
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-Related structure data
Related structure data | 3ichC 1cynS C: citing same article (ref.) 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: 20735.787 Da / Num. of mol.: 2 / Fragment: UNP residues 34-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIB, CYPB / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23284, peptidylprolyl isomerase #2: Protein/peptide | | Mass: 4342.601 Da / Num. of mol.: 1 / Fragment: P-domain fragment: residues 317-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: CANX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: PDB-D9N169, UniProt: E2RA18*PLUS #3: Chemical | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE SEQUENCE OF ENTITY 2 (CHAIN C) CORRESPONDS TO RESIDUES 317-350 OF DOG ...AUTHORS STATE THAT THE SEQUENCE OF ENTITY 2 (CHAIN C) CORRESPOND | |
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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: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22% w/v PEG 8000, 10mM ZnCl2, 0.1M Tris buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9995 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9995 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 38845 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2598 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CYN Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.316 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.291 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.75 Å / Total num. of bins used: 20
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