+Open data
-Basic information
Entry | Database: PDB / ID: 6mtv | |||||||||
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Title | Crystal structure of human Scribble PDZ1:MCC complex | |||||||||
Components |
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Keywords | CELL ADHESION / Cell Polarity / MCC / PDZ domain | |||||||||
Function / homology | Function and homology information neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / 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 ...neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / 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 / negative regulation of epithelial cell migration / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / 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 / receptor clustering / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / immunological synapse / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / establishment of protein localization / negative regulation of canonical Wnt signaling pathway / cytoplasmic ribonucleoprotein granule / cell-cell adhesion / Wnt signaling pathway / negative regulation of epithelial cell proliferation / cell migration / cell-cell junction / positive regulation of type II interferon production / presynapse / signaling receptor activity / cell junction / lamellipodium / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / signal transduction / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å | |||||||||
Authors | Caria, S. / Stewart, B.Z. / Humbert, P.O. / Kvansakul, M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Febs J. / Year: 2019 Title: Structural analysis of phosphorylation-associated interactions of human MCC with Scribble PDZ domains. Authors: Caria, S. / Stewart, B.Z. / Jin, R. / Smith, B.J. / 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 | 6mtv.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mtv.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 6mtv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/6mtv ftp://data.pdbj.org/pub/pdb/validation_reports/mt/6mtv | HTTPS FTP |
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-Related structure data
Related structure data | 6mtuC 5vwiS 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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-Components
#1: Protein | Mass: 12437.953 Da / Num. of mol.: 2 / Fragment: residues 700-816 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli (E. coli) / References: UniProt: Q14160 #2: Protein/peptide | Mass: 898.937 Da / Num. of mol.: 2 / Fragment: residues 822-829 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P23508*PLUS #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-SO4 / #5: 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: 3.28 Å3/Da / Density % sol: 62.51 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: polyethylene glycol 1000, lithium sulfate monohydrate, phosphate/citrate |
-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: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2017 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→39.253 Å / Num. obs: 5477 / % possible obs: 97.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 23.59 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.072 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.59→2.71 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 0.553 / Num. unique obs: 617 / CC1/2: 0.553 / Rpim(I) all: 0.975 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VWI Resolution: 2.597→39.253 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.07 / 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 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.597→39.253 Å
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Refine LS restraints |
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LS refinement shell |
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