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Yorodumi- PDB-4jor: CFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncopro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jor | ||||||
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Title | CFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncoprotein C-terminal peptide (RLQRRRETQV) | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / PDZ / CFTR Associated Ligand / CAL / PIST / FIG / Human papillomavirus type 18 / HPV18 / E6 oncoprotein | ||||||
Function / homology | Function and homology information negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport ...negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / PDZ domain binding / protein transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / transmembrane transporter binding / host cell cytoplasm / postsynaptic density / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / lysosomal membrane / Golgi membrane / virus-mediated perturbation of host defense response / negative regulation of DNA-templated transcription / DNA-templated transcription / dendrite / host cell nucleus / Golgi apparatus / protein-containing complex / DNA binding / zinc ion binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human papillomavirus type 18 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Amacher, J.F. / Madden, D.R. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Stereochemical Preferences Modulate Affinity and Selectivity among Five PDZ Domains that Bind CFTR: Comparative Structural and Sequence Analyses. Authors: Amacher, J.F. / Cushing, P.R. / Brooks, L. / Boisguerin, P. / Madden, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jor.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jor.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jor_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 4jor_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 4jor_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4jor_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/4jor ftp://data.pdbj.org/pub/pdb/validation_reports/jo/4jor | HTTPS FTP |
-Related structure data
Related structure data | 4joeC 4jofC 4jogC 4johC 4jojC 4jokC 4jopC 4k6yC 4k72C 4k75C 4k76C 4k78C 4e34S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9353.722 Da / Num. of mol.: 2 / Fragment: CAL PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9HD26 #2: Protein/peptide | Mass: 1345.554 Da / Num. of mol.: 2 / Fragment: HPV18 E6 peptide / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 18 / References: UniProt: P06463 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 1.92 Å3/Da / Density % sol: 36.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 29% (w/v) polyethylene glycol (PEG), 0.075 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 29, 2012 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.34→19.29 Å / Num. all: 36592 / Num. obs: 34483 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 7.53 / Rmerge(I) obs: 0.05 / Rsym value: 0.038 / Net I/σ(I): 36.69 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4E34 (CAL PDZ domain bound to iCAL36 peptide) Resolution: 1.34→19.29 Å / SU ML: 0.16 / Cross valid method: Omit map / σ(F): 2 / σ(I): 7.53 / Phase error: 17.36 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.62 Å2 / ksol: 0.45 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.34→19.29 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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