+Open data
-Basic information
Entry | Database: PDB / ID: 5e6p | ||||||||||||
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Title | PlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Plexin / PDZ / PDZ-RhoGEF / Complex | ||||||||||||
Function / homology | Function and homology information excitatory synapse assembly / semaphorin-plexin signaling pathway involved in axon guidance / regulation of neuron migration / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / positive regulation of axonogenesis / RHOB GTPase cycle ...excitatory synapse assembly / semaphorin-plexin signaling pathway involved in axon guidance / regulation of neuron migration / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / positive regulation of axonogenesis / RHOB GTPase cycle / establishment of cell polarity / regulation of GTPase activity / NRAGE signals death through JNK / homophilic cell adhesion via plasma membrane adhesion molecules / RHOC GTPase cycle / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / neuroblast proliferation / RHOA GTPase cycle / striated muscle contraction / regulation of cell migration / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / positive regulation of translation / G protein-coupled receptor binding / neural tube closure / regulation of cell growth / regulation of protein phosphorylation / brain development / positive regulation of neuron projection development / G alpha (12/13) signalling events / regulation of cell shape / actin cytoskeleton organization / collagen-containing extracellular matrix / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.215 Å | ||||||||||||
Authors | Pascoe, H.G. / Zhang, X. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ-RhoGEF. Authors: Pascoe, H.G. / Gutowski, S. / Chen, H. / Brautigam, C.A. / Chen, Z. / Sternweis, P.C. / Zhang, X. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e6p.cif.gz | 247.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e6p.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 5e6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/5e6p ftp://data.pdbj.org/pub/pdb/validation_reports/e6/5e6p | HTTPS FTP |
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-Related structure data
Related structure data | 3ig3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 71868.688 Da / Num. of mol.: 1 / Fragment: UNP residues 1226-1842 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxnb2 / Plasmid: pskb2 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: B2RXS4 |
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#2: Protein | Mass: 9227.785 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 42-125) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380 / Plasmid: pskb2 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: O15085 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 0.2 M K/Na tartrate, 0.1 M Na citrate pH 5.3, 1.4 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979237 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979237 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 16847 / % possible obs: 99.9 % / Redundancy: 30.1 % / Biso Wilson estimate: 130.9 Å2 / Rsym value: 0.099 / Net I/σ(I): 56 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 27.4 % / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IG3 Resolution: 3.215→48.53 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 38.85 / 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: 3.215→48.53 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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