+Open data
-Basic information
Entry | Database: PDB / ID: 4q2q | ||||||
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Title | ZO1 PDZ3 in Complex with a Phage-Derived Peptide | ||||||
Components | Tight junction protein ZO-1 | ||||||
Keywords | PROTEIN BINDING / PDZ | ||||||
Function / homology | Function and homology information positive regulation of blood-brain barrier permeability / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / RUNX1 regulates expression of components of tight junctions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of endothelial intestinal barrier / protein localization to cell-cell junction / regulation of cell junction assembly / protein localization to adherens junction / Regulation of gap junction activity ...positive regulation of blood-brain barrier permeability / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / RUNX1 regulates expression of components of tight junctions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of endothelial intestinal barrier / protein localization to cell-cell junction / regulation of cell junction assembly / protein localization to adherens junction / Regulation of gap junction activity / protein localization to bicellular tight junction / gap junction / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / tight junction / actomyosin structure organization / podosome / Signaling by Hippo / regulation of bicellular tight junction assembly / cell-cell junction assembly / negative regulation of stress fiber assembly / apical junction complex / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / regulation of cytoskeleton organization / bicellular tight junction / cell adhesion molecule binding / cell projection / adherens junction / cell-cell adhesion / apical part of cell / cell junction / actin cytoskeleton organization / basolateral plasma membrane / calmodulin binding / positive regulation of cell migration / cadherin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein-containing complex / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||
Authors | Appleton, B.A. / Wiesmann, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: A structural portrait of the PDZ domain family. Authors: Ernst, A. / Appleton, B.A. / Ivarsson, Y. / Zhang, Y. / Gfeller, D. / Wiesmann, C. / Sidhu, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q2q.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q2q.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 4q2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q2q_validation.pdf.gz | 415.2 KB | Display | wwPDB validaton report |
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Full document | 4q2q_full_validation.pdf.gz | 416.3 KB | Display | |
Data in XML | 4q2q_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 4q2q_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q2q ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q2q | HTTPS FTP |
-Related structure data
Related structure data | 4q2nC 4q2oC 4q2pC 2h3lS 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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Unit cell |
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-Components
#1: Protein | Mass: 11065.695 Da / Num. of mol.: 1 / Fragment: unp residues 419-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TJP1, ZO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07157 |
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#2: Water | ChemComp-HOH / |
Sequence details | PHAGE-DERIVED PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.5 Details: 0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 6, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→50 Å / Num. obs: 18660 / % possible obs: 99.1 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.032 / Χ2: 1.07 / Net I/σ(I): 58.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2h3l Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.502 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.32 Å2 / Biso mean: 26.2068 Å2 / Biso min: 14.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.451→1.48 Å / Total num. of bins used: 25
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