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- PDB-2omj: solution structure of LARG PDZ domain -

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Basic information

Entry
Database: PDB / ID: 2omj
Titlesolution structure of LARG PDZ domain
ComponentsRho guanine nucleotide exchange factor 12
KeywordsCELL ADHESION / nerve system development / actin reorganization
Function / homology
Function and homology information


Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity ...Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G alpha (12/13) signalling events / G protein-coupled receptor signaling pathway / extracellular exosome / 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 / ARHGEF1-like, PH domain / PH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / RGS, subdomain 2 / RGS domain superfamily ...ARHGEF12, PH domain / LARG, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / ARHGEF1-like, PH domain / PH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / RGS, subdomain 2 / RGS domain superfamily / 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. / 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 / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
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. / Hu, Q.
CitationJournal: To be Published
Title: solution structure and dynamics of the LARG PDZ domain
Authors: Liu, J. / Huang, H.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 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
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 12


Theoretical massNumber of molelcules
Total (without water)9,3701
Polymers9,3701
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
Representative

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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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCANH
121CBCA(CO)NH
131HBHA(CBCACO)NH
141HNCO
2523D 13C-separated NOESY
262(H)CCH-TOCSY
272(H)CCH-COSY
1813D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM LARG PDZ domain, 15N, 13C-labeled, 5mM EDTA, 1mM EDTA, 50mM phosphate buffer, 90% H2O, 10% D2O50mM phosphate buffer, 90% H2O, 10% D2O
21.3mM LARG PDZ domain, 15N, 13C-labeled, 5mM EDTA, 1mM EDTA, 50mM phosphate buffer, 99.9% D2O50mM phosphate buffer, 99.9% D2O
Sample conditionsIonic strength: 50mM 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
NameDeveloperClassification
cns1.1A.T.Brungerstructure solution
Csi 1.0David S. Wishartprocessing
Sparky 3T.D.Goddard and D.G.Knellerdata analysis
Nmrpipe 2.2F.Delaglioprocessing
Molmol 2k.2Koradidata analysis
cns1.1A.T.Brungerrefinement
RefinementMethod: Distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: A total of 1145 experimental distance restraint derived from NOE and hydrogen bonds and 82 dihedral angle restraints were utilized in the structure calculations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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