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- PDB-1wfw: Solution structure of SH3 domain of mouse Kalirin-9a protein -

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Basic information

Entry
Database: PDB / ID: 1wfw
TitleSolution structure of SH3 domain of mouse Kalirin-9a protein
ComponentsKalirin-9a
KeywordsSIGNALING PROTEIN / SH3 domain / neuron-specific GDP/GTP exchange factor / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


RHOA GTPase cycle / EPHB-mediated forward signaling / maternal process involved in parturition / NRAGE signals death through JNK / RAC1 GTPase cycle / RHOG GTPase cycle / modification of postsynaptic actin cytoskeleton / G alpha (q) signalling events / G alpha (12/13) signalling events / regulation of dendrite development ...RHOA GTPase cycle / EPHB-mediated forward signaling / maternal process involved in parturition / NRAGE signals death through JNK / RAC1 GTPase cycle / RHOG GTPase cycle / modification of postsynaptic actin cytoskeleton / G alpha (q) signalling events / G alpha (12/13) signalling events / regulation of dendrite development / NMDA selective glutamate receptor signaling pathway / negative regulation of growth hormone secretion / MAPK6/MAPK4 signaling / positive regulation of dendritic spine morphogenesis / regulation of modification of postsynaptic actin cytoskeleton / habituation / maternal behavior / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / extrinsic component of membrane / neuromuscular junction development / social behavior / lactation / axonogenesis / adult locomotory behavior / guanyl-nucleotide exchange factor activity / axon guidance / memory / presynapse / nervous system development / postsynaptic density / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Spectrin repeat ...Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / 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. / SH3 Domains / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Fibronectin type III domain / SH3 domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of SH3 domain of mouse Kalirin-9a protein
Authors: Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kalirin-9a


Theoretical massNumber of molelcules
Total (without water)7,6361
Polymers7,6361
Non-polymers00
Water0
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, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Kalirin-9a / unnamed protein product


Mass: 7636.433 Da / Num. of mol.: 1 / Fragment: SH3 domain / Mutation: S209G, K237E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 2210407G14 / Plasmid: P030120-92 / References: GenBank: 12843281, UniProt: A2CG49*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM SH3 domain U-15N, 13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.8994Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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