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- PDB-6ubh: Structure of the MM7 Erbin PDZ variant in complex with a high-aff... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ubh | ||||||
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Title | Structure of the MM7 Erbin PDZ variant in complex with a high-affinity peptide | ||||||
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![]() | SIGNALING PROTEIN / Phage display / directed evolution / -2 position / specificity / phage library | ||||||
Function / homology | ![]() 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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Singer, A.U. / Teyra, J. / McLaughlin, M. / Ernst, A. / Sicheri, F. / Sidhu, S.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Comprehensive Assessment of the Relationship Between Site -2 Specificity and Helix alpha 2 in the Erbin PDZ Domain. Authors: Teyra, J. / McLaughlin, M. / Singer, A. / Kelil, A. / Ernst, A. / Sicheri, F. / Sidhu, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97 KB | Display | ![]() |
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PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 251.1 KB | Display | ![]() |
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Full document | ![]() | 251 KB | Display | |
Data in XML | ![]() | 1 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lulC ![]() 6ubg S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10315.668 Da / Num. of mol.: 4 / Mutation: H1347M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): 6His and GST at N-terminus followed by TEV cleavage site Production host: ![]() ![]() #2: Protein/peptide | Mass: 956.074 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 7% PEG8K, 100 mM Sodium Acetate pH 4.5 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 6, 2018 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 26382 / % possible obs: 78.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.019 / Rrim(I) all: 0.29 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.053 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 6175 / CC1/2: 0.991 / Rpim(I) all: 0.048 / Rrim(I) all: 0.071 / % possible all: 58.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6UBG ![]() 6ubg Resolution: 1.8→36.77 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 16.76 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.77 Å
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LS refinement shell | Resolution: 1.8→1.853 Å
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