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- PDB-1u3o: Solution structure of rat Kalirin N-terminal SH3 domain -

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Basic information

Entry
Database: PDB / ID: 1u3o
TitleSolution structure of rat Kalirin N-terminal SH3 domain
ComponentsHuntingtin-associated protein-interacting protein
KeywordsSIGNALING PROTEIN / SH3 / cis-Proline
Function / homology
Function and homology information


RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / MAPK6/MAPK4 signaling / RAC1 GTPase cycle / maternal process involved in parturition / RHOA GTPase cycle / habituation / modification of postsynaptic actin cytoskeleton / regulation of dendrite development ...RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / MAPK6/MAPK4 signaling / RAC1 GTPase cycle / maternal process involved in parturition / RHOA GTPase cycle / habituation / modification of postsynaptic actin cytoskeleton / regulation of dendrite development / NMDA selective glutamate receptor signaling pathway / negative regulation of growth hormone secretion / positive regulation of dendritic spine morphogenesis / EPHB-mediated forward signaling / regulation of modification of postsynaptic actin cytoskeleton / maternal behavior / G alpha (q) signalling events / 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 / ATP binding / metal ion binding / 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 / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / 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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / Torsion angle dynamics, simulated annealing
AuthorsSchiller, M.R. / Chakrabarti, K. / King, G.F. / Schiller, N.I. / Eipper, B.A. / Maciejewski, M.W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Regulation of RhoGEF Activity by Intramolecular and Intermolecular SH3 Domain Interactions.
Authors: Schiller, M.R. / Chakrabarti, K. / King, G.F. / Schiller, N.I. / Eipper, B.A. / Maciejewski, M.W.
History
DepositionJul 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Huntingtin-associated protein-interacting protein


Theoretical massNumber of molelcules
Total (without water)8,5791
Polymers8,5791
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Huntingtin-associated protein-interacting protein / DUO protein / Kalirin / PAM COOH-terminal interactor protein 10 / P-CIP10


Mass: 8578.576 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kalirin, HAPIP, Duo / Organ: brain / Plasmid: pGEX6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97924

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
121HNHB
1323D HN(COCA)CB
1423D C(CO)NH-TOCSY
1523D 15N NOESY-HSQC
1623D 13C HSQC-NOESY
1723D HN(CA)CB
182HC(CO)NH-TOCSY
192(H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM U-15N protein, 50 mM HEPES, 150 mM NaCl, 1 mM dithiotheitol, 92.5% H2O, 7.5% D2O92.5% H2O, 7.5% D2O
21 mM U-15N,13C protein, 50 mM HEPES, 150 mM NaCl, 1 mM dithiotheitol, 92.5% H2O, 7.5% D2O92.5% H2O, 7.5% D2O
Sample conditionsIonic strength: 200 mM / pH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P., Mumenthaler, C., and Wuthrich, K.structure solution
CYANA1.0.0Guntert,P.,structure solution
X-PLOR3.851Brunger, A.T.refinement
NMRPipe2.3Delaglio,F., Grzesiek,S., Vuister,G.W., Zhu,G., Pfeifer,J., and Bax,A.processing
XEASY1.4Bartels,C., Xia,T., Billeter,M., Guntert,P., and Wuthrich,K.data analysis
TALOSCornilescu,G., Delaglio,F., and Bax,A.structure solution
RefinementMethod: Torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The structure is based on a total of 1017 restraints, with 893 NOE-derived distance constraints, 102 dihedral angle restraints, and 22 hydrogen bond restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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