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- PDB-2os6: Solution structure of LARG PDZ domain in complex with C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 2os6
TitleSolution structure of LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1
Components
  • C-terminal peptide of Plexin-B1
  • Rho guanine nucleotide exchange factor 12
KeywordsCELL ADHESION / nerve system development / cytoskeleton rearrangement
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 / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / RHOB GTPase cycle / positive regulation of axonogenesis / NRAGE signals death through JNK / RHOC GTPase cycle / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / regulation of cell migration / GTPase activator activity / guanyl-nucleotide exchange factor activity / neuron projection morphogenesis / G protein-coupled receptor binding / 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 / G protein-coupled receptor signaling pathway / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ARHGEF12, PH domain / LARG, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain ...ARHGEF12, PH domain / LARG, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / ARHGEF1-like, PH domain / PH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / RGS, subdomain 2 / Plexin family / RGS domain superfamily / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / IPT domain / PDZ domain / Pdz3 Domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Immunoglobulin E-set / PH-like domain superfamily / Roll / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Plexin-B1 / Rho guanine nucleotide exchange factor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsLiu, J. / Huang, H. / Yang, Y.
CitationJournal: To be Published
Title: Solution structure of the LARG PDZ domain in complex with C-terminal peptide of Plexin B1
Authors: Liu, J. / Huang, H. / Yang, Y.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 12
B: C-terminal peptide of Plexin-B1


Theoretical massNumber of molelcules
Total (without water)10,2882
Polymers10,2882
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Rho guanine nucleotide exchange factor 12 / LARG protein / Leukemia-associated RhoGEF


Mass: 9369.684 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b (+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NZN5
#2: Protein/peptide C-terminal peptide of Plexin-B1 / Semaphorin receptor SEP


Mass: 918.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: O43157

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1322D, 13C, 15N-filtered, 13C-edited NOESY
142DQF-COSY
1522D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 90% H2O, 10% D2O50mM phosphate buffer, 90% H2O, 10% D2O
20.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 99.9% D2O50mM phosphate buffer, 99.9% D2O
Sample conditionsIonic strength: 50 mM phosphate buffer, 50mM NaCl / pH: 6.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSCns 1.1Brunger A. T. etallstructure solution
NMRPipeNmrpipe 2.2F.Delaglioprocessing
Sparky 3Sparky 3T.D.Goddard and D.G.Knellerdata analysis
Molmol 2k.2Molmol 2k.2Koradiprocessing
Csi 1.0Csi 1.0David S. Wishartrefinement
RefinementMethod: Distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The complex structure is solved using a total of 1306 experimental restraints that include 1155 intramolecular NOEs, 90 dihedral angle restraints and 61 intermolecular NOEs derived from NMR spectroscopy
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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