|Entry||Database: PDB / ID: 2jph|
|Title||NMR solution structure of the Rho GTPase binding domain of human plexin-b1|
|Keywords||SIGNALING PROTEIN / PROTEIN BINDING / protein / ubiquitin fold|
|Function / homology|
Function and homology information
semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis / semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / semaphorin receptor complex / inhibitory synapse assembly / Sema4D induced cell migration and growth-cone collapse / semaphorin receptor activity / RHOD GTPase cycle / ossification involved in bone maturation ...semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis / semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / semaphorin receptor complex / inhibitory synapse assembly / Sema4D induced cell migration and growth-cone collapse / semaphorin receptor activity / RHOD GTPase cycle / ossification involved in bone maturation / negative regulation of cell adhesion / Sema4D mediated inhibition of cell attachment and migration / GTPase activating protein binding / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / positive regulation of axonogenesis / regulation of GTPase activity / neuron projection morphogenesis / regulation of cell migration / GTPase activator activity / G alpha (12/13) signalling events / positive regulation of GTPase activity / transmembrane signaling receptor activity / positive regulation of phosphatidylinositol 3-kinase signaling / cell migration / regulation of cell shape / intracellular signal transduction / plasma membrane => GO:0005886 / extracellular region / plasma membrane
Similarity search - Function
Plexin, TIG domain 2 / TIG domain found in plexin / TIG domain / Plexin, TIG domain 1 / Plexin cytoplasmic RasGAP domain / Plexin, cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain ...Plexin, TIG domain 2 / TIG domain found in plexin / TIG domain / Plexin, TIG domain 1 / Plexin cytoplasmic RasGAP domain / Plexin, cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain profile. / Sema domain superfamily / Sema domain / IPT/TIG domain / Rho GTPase activation protein / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Roll / Alpha Beta
Similarity search - Domain/homology
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||SOLUTION NMR / torsion angle dynamics, simulated annealing|
|Authors||Tong, Y. / Buck, M.|
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.
|Structure viewer||Molecule: |
Downloads & links
|#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) (unknown) / Strain (production host): BL21 (DE3) / References: UniProt: O43157
|Experiment||Method: SOLUTION NMR|
|Sample conditions||Ionic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K|
|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
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