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Yorodumi- PDB-6q0n: Structure of the Erbin PDB domain in complex with a high-affinity... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q0n | ||||||
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Title | Structure of the Erbin PDB domain in complex with a high-affinity peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / high-affinity / specificity | ||||||
Function / homology | Function and homology information basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / neurotransmitter receptor transport postsynaptic membrane to endosome / embryo development / neurotransmitter receptor transport, endosome to postsynaptic membrane / intermediate filament cytoskeleton organization / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity ...basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / neurotransmitter receptor transport postsynaptic membrane to endosome / embryo development / neurotransmitter receptor transport, endosome to postsynaptic membrane / intermediate filament cytoskeleton organization / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity / RHOB GTPase cycle / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / negative regulation of NF-kappaB transcription factor activity / RHOC GTPase cycle / receptor clustering / response to muramyl dipeptide / RHOG GTPase cycle / basement membrane / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / protein targeting / Signaling by ERBB2 / RAC1 GTPase cycle / Constitutive Signaling by Overexpressed ERBB2 / basal plasma membrane / integrin-mediated signaling pathway / adherens junction / Signaling by ERBB2 TMD/JMD mutants / Signaling by ERBB2 ECD mutants / neuromuscular junction / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / structural constituent of cytoskeleton / Downregulation of ERBB2 signaling / cell-cell adhesion / cell junction / cellular response to tumor necrosis factor / basolateral plasma membrane / postsynaptic membrane / nuclear membrane / response to lipopolysaccharide / postsynaptic density / cell adhesion / nuclear speck / signaling receptor binding / glutamatergic synapse / signal transduction / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Singer, A.U. / Teyra, J. / Ernst, A. / Sicheri, F. / Sidhu, S.S. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Comprehensive analysis of all evolutionary paths between two divergent PDZ domain specificities. Authors: Teyra, J. / Ernst, A. / Singer, A. / Sicheri, F. / 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 | 6q0n.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q0n.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 6q0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q0n_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 6q0n_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 6q0n_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 6q0n_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/6q0n ftp://data.pdbj.org/pub/pdb/validation_reports/q0/6q0n | HTTPS FTP |
-Related structure data
-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: 10148.464 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERBIN, ERBB2IP, KIAA1225, LAP2 / Plasmid: pHH0103 Details (production host): 6-His and GST at N-terminus, followed by TEV cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RT1 #2: Protein/peptide | Mass: 854.903 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: 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: 1.81 Å3/Da / Density % sol: 31.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 6%PEG3350, 100 mM MgCl2, 100 mM Sodium Acetate pH 4.5. Cryoprotection was achieved with the same buffer plus 25% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2018 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→30.04 Å / Num. obs: 47892 / % possible obs: 86.7 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.16→1.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1996 / CC1/2: 0.856 / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SWISS-MODELLER model of the E-14 variant of the Erbin PDZ Resolution: 1.18→30.04 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 27.9 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→30.04 Å
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LS refinement shell | Resolution: 1.18→1.1934 Å
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