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Yorodumi- PDB-2jph: NMR solution structure of the Rho GTPase binding domain of human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jph | ||||||
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Title | NMR solution structure of the Rho GTPase binding domain of human plexin-b1 | ||||||
Components | Plexin-B1 | ||||||
Keywords | SIGNALING PROTEIN / PROTEIN BINDING / protein / ubiquitin fold | ||||||
Function / homology | Function and homology information semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding ...semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / regulation of cell migration / GTPase activator activity / neuron projection morphogenesis / positive regulation of GTPase activity / G alpha (12/13) signalling events / cell migration / transmembrane signaling receptor activity / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Authors | Tong, Y. / Buck, M. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Insights into Oncogenic Mutations of Plexin-B1 Based on the Solution Structure of the Rho GTPase Binding Domain Authors: Tong, Y. / Hota, P.K. / Hamaneh, M.B. / Buck, M. #1: Journal: Structure / Year: 2005 Title: When monomers are preferred: a strategy for the identification and disruption of weakly oligomerized proteins. Authors: Tong, Y. / Hughes, D. / Placanica, L. / Buck, M. #2: Journal: J.Biomol.NMR / Year: 2005 Title: 1H, 15N and 13C Resonance assignments and secondary structure determination reveal that the minimal Rac1 GTPase binding domain of plexin-B1 has a ubiquitin fold. Authors: Tong, Y. / Buck, M. #3: Journal: Science / Year: 2004 Title: The Semaphorin 4D receptor Plexin-B1 is a GTPase activating protein for R-Ras. Authors: Oinuma, I. / Ishikawa, Y. / Katoh, H. / Negishi, M. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The semaphorin receptor plexin-B1 specifically interacts with active Rac in a ligand-dependent manner. Authors: Vikis, H.G. / Li, W. / He, Z. / Guan, K.L. #5: Journal: CURR.BIOL. / Year: 2001 Title: Plexin-B semaphorin receptors interact directly with active Rac and regulate the actin cytoskeleton by activating Rho. Authors: Driessens, M.H. / Nobes, C.D. / Self, A. / Jordens, I. / Goodman, C.S. / Hall, A. #6: Journal: J.Biol.Chem. / Year: 2007 Title: Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain Authors: Tong, Y. / Chugha, P. / Hota, P.K. / Alviani, R.S. / Li, M. / Tempel, W. / Shen, L. / Park, H.W. / Buck, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jph.cif.gz | 743.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jph.ent.gz | 624.3 KB | Display | PDB format |
PDBx/mmJSON format | 2jph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/2jph ftp://data.pdbj.org/pub/pdb/validation_reports/jp/2jph | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13590.607 Da / Num. of mol.: 1 / Fragment: Sequence database residues 1743-1862 / Mutation: W1830F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, SEP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O43157 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 Details: Following Nederveen AJ et al., Proteins 2005, 59: 662-672 but in presence of a 10angstrom explicit water shell, final minimization in presence of 4.5 Angstrom explicit water shell | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |