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Yorodumi- PDB-8b9t: Crystal structure of Scribble PDZ1 with human papillomavirus stra... -
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-Basic information
Entry | Database: PDB / ID: 8b9t | |||||||||
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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 / astrocyte cell migration ...: / 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 / PDZ domain binding / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / cell junction / lamellipodium / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / basolateral plasma membrane / symbiont-mediated perturbation of host ubiquitin-like protein modification / cell population proliferation / host cell cytoplasm / postsynaptic density / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / positive regulation of apoptotic process / DNA-templated transcription / glutamatergic synapse / host cell nucleus / regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Human papillomavirus type 16 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 8b9t.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b9t.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 8b9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b9t_validation.pdf.gz | 464.3 KB | Display | wwPDB validaton report |
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Full document | 8b9t_full_validation.pdf.gz | 466.6 KB | Display | |
Data in XML | 8b9t_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 8b9t_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/8b9t ftp://data.pdbj.org/pub/pdb/validation_reports/b9/8b9t | HTTPS FTP |
-Related structure data
Related structure data | 8b82C 8b87C 8b8oC 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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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 10082.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: At the n-terminal of chain 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 |
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#2: Protein/peptide | Mass: 1236.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16 / References: UniProt: A0A384KQK8 |
-Non-polymers , 4 types, 32 molecules
#3: Chemical | ChemComp-NA / | ||||
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#4: Chemical | ChemComp-EPE / #5: Chemical | ChemComp-IPA / | #6: Water | ChemComp-HOH / | |
-Details
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: 5.17 Å3/Da / Density % sol: 76.19 % / Description: hexagonal dipyramid |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.5 M NaCl, 0.1 m Na HEPES pH 8.0 / PH range: 7.0-8.0 |
-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: Aug 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→37.23 Å / Num. obs: 7707 / % possible obs: 99.44 % / Redundancy: 6.2 % / Biso Wilson estimate: 65.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1008 / Net I/σ(I): 23.29 |
Reflection shell | Resolution: 2.5→2.589 Å / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 732 / CC1/2: 0.939 / % possible all: 97.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XA6 Resolution: 2.5→37.23 Å / SU ML: 0.3352 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.2697 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: 72.32 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→37.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 29.4120609011 Å / Origin y: -11.862134485 Å / Origin z: 3.9200487087 Å
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Refinement TLS group | Selection details: all |