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- PDB-2jph: NMR solution structure of the Rho GTPase binding domain of human ... -

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Basic information

Entry
Database: PDB / ID: 2jph
TitleNMR solution structure of the Rho GTPase binding domain of human plexin-b1
ComponentsPlexin-B1
KeywordsSIGNALING PROTEIN / PROTEIN BINDING / protein / ubiquitin fold
Function / homology
Function and homology information


semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / positive regulation of axonogenesis / inhibitory synapse assembly / GTPase activating protein binding ...semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / positive regulation of axonogenesis / inhibitory synapse assembly / GTPase activating protein binding / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of Rho protein signal transduction / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / positive regulation of GTPase activity / synapse assembly / neuron projection morphogenesis / GTPase activator activity / regulation of cell migration / transmembrane signaling receptor activity / cell migration / G alpha (12/13) signalling events / regulation of cell shape / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / glutamatergic synapse / extracellular region / plasma membrane
Similarity search - Function
Plexin-B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain ...Plexin-B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsTong, 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
DepositionMay 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plexin-B1


Theoretical massNumber of molelcules
Total (without water)13,5911
Polymers13,5911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Plexin-B1 / Semaphorin receptor SEP


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.75 mM [U-100% 13C; U-100% 15N] protein, 90%H2O/10% D2O90% H2O/10% D2O
21.25 mM [U-100% 13C; U-100% 15N; 80% 2H] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMentity[U-100% 13C; U-100% 15N]1
1.0 mMentity[U-100% 13C; U-100% 15N; 80% 2H]2
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANA2.3Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.3Guntert, Mumenthaler and Wuthrichgeometry optimization
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: 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 representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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