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Yorodumi- PDB-4nmq: CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nmq | ||||||
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Title | CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(Ac-K-4) (ANSRW[Ac-K]TSII) | ||||||
Components |
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Keywords | protein transport/inhibitor / CAL / PIST / GOPC / FIG / PDZ / CFTR / CFTR associated ligand / PDZ-peptide / protein transport-inhibitor complex | ||||||
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 / protein transport / transmembrane transporter binding / postsynaptic density / Golgi membrane / lysosomal membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Amacher, J.F. / Madden, D.R. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Chemically Modified Peptide Scaffolds Target the CFTR-Associated Ligand PDZ Domain. Authors: Amacher, J.F. / Zhao, R. / Spaller, M.R. / 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 | 4nmq.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nmq.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 4nmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nmq_validation.pdf.gz | 464 KB | Display | wwPDB validaton report |
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Full document | 4nmq_full_validation.pdf.gz | 466.3 KB | Display | |
Data in XML | 4nmq_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 4nmq_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/4nmq ftp://data.pdbj.org/pub/pdb/validation_reports/nm/4nmq | HTTPS FTP |
-Related structure data
Related structure data | 4nmoC 4nmpC 4nmrC 4nmsC 4nmtC 4nmvC 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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Details | CAL PDZ domain bound to decameric peptide |
-Components
#1: Protein | Mass: 9353.722 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 284-370 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 | #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: 1.93 Å3/Da / Density % sol: 36.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 40% (w/v) polyethylene glycol (PEG), 0.15 M sodium chloride, 0.1 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: 0.8856 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 18, 2011 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→19.7 Å / Num. all: 33017 / Num. obs: 32997 / % possible obs: 99.9 % / Observed criterion σ(F): 6.3 / Observed criterion σ(I): 23.24 / Rsym value: 0.063 / Net I/σ(I): 23.24 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4E34 Resolution: 1.4→19.737 Å / SU ML: 0.19 / σ(F): 2.02 / Phase error: 16.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.366 Å2 / ksol: 0.415 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.4→19.737 Å
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Refine LS restraints |
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LS refinement shell |
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