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Yorodumi- PDB-8b8o: Crystal structure of Scribble PDZ1 with human papillomavirus stra... -
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-Basic information
Entry | Database: PDB / ID: 8b8o | |||||||||
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Title | Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide | |||||||||
Components |
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Keywords | PROTEIN BINDING / Scribble / human papillomavirus / E6 / PDZ domain / cell polarity | |||||||||
Function / homology | Function and homology information : / : / extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex ...: / : / extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / protein localization to adherens junction / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / cell junction / lamellipodium / basolateral plasma membrane / cell population proliferation / host cell cytoplasm / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / host cell nucleus / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) human papillomavirus 66 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Stewart, B.Z. / Kvansakul, M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: To Be Published Title: Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide Authors: Stewart, B.Z. / Caria, S. / Humbert, P.O. / Kvansakul, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b8o.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b8o.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 8b8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b8o_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 8b8o_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 8b8o_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 8b8o_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/8b8o ftp://data.pdbj.org/pub/pdb/validation_reports/b8/8b8o | HTTPS FTP |
-Related structure data
Related structure data | 8b82C 8b87C 8b9tC 8biaC 8bj0C 6xa6S S: Starting model for refinement C: citing same article (ref.) |
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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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.964038778597, 0.123768590064, -0.23518199224), (0.0639915060671, -0.967003924289, -0.246593790595), (-0.257942475199, 0.222676326812, -0.940149420553)Vector: 4. ...NCS oper: (Code: given Matrix: (0.964038778597, 0.123768590064, -0.23518199224), Vector: |
-Components
#1: Protein | Mass: 10082.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: At the n-terminal of chain A, B, the sequence GPLGS is part of the expression tag Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon+ / References: UniProt: Q14160 #2: Protein/peptide | Mass: 1080.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) human papillomavirus 66 / References: UniProt: G8HXP2 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.37 Å3/Da / Density % sol: 48.16 % / Description: Diamond plate |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 0.1 M Na HEPES pH 7.9, 63% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→32.03 Å / Num. obs: 4654 / % possible obs: 99.57 % / Redundancy: 7 % / Biso Wilson estimate: 84.26 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1438 / Net I/σ(I): 8.41 |
Reflection shell | Resolution: 2.9→3.004 Å / Rmerge(I) obs: 1.293 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 451 / CC1/2: 0.594 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XA6 Resolution: 2.9→32.03 Å / SU ML: 0.5153 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5046 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.69 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→32.03 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 3.10947417099 Å | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 21.3400575757 Å / Origin y: -25.5439849334 Å / Origin z: 1.20771914627 Å
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Refinement TLS group | Selection details: all |