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- PDB-2kr9: Kalirin DH1 NMR structure -

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Basic information

Entry
Database: PDB / ID: 2kr9
TitleKalirin DH1 NMR structure
ComponentsKalirin
KeywordsTRANSFERASE / Dbl-family GEF / Rho GTPase GEF / Cytoskeleton / Disulfide bond / Guanine-nucleotide releasing factor / Immunoglobulin domain / Kinase
Function / homology
Function and homology information


RHOG GTPase cycle / NRAGE signals death through JNK / MAPK6/MAPK4 signaling / G alpha (12/13) signalling events / maternal process involved in parturition / RAC1 GTPase cycle / RHOA GTPase cycle / modification of postsynaptic actin cytoskeleton / habituation / regulation of modification of postsynaptic actin cytoskeleton ...RHOG GTPase cycle / NRAGE signals death through JNK / MAPK6/MAPK4 signaling / G alpha (12/13) signalling events / maternal process involved in parturition / RAC1 GTPase cycle / RHOA GTPase cycle / modification of postsynaptic actin cytoskeleton / habituation / regulation of modification of postsynaptic actin cytoskeleton / negative regulation of growth hormone secretion / NMDA selective glutamate receptor signaling pathway / positive regulation of dendritic spine morphogenesis / regulation of dendrite development / EPHB-mediated forward signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / maternal behavior / G alpha (q) signalling events / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / social behavior / lactation / extrinsic component of membrane / adult locomotory behavior / axonogenesis / guanyl-nucleotide exchange factor activity / central nervous system development / presynapse / memory / axon guidance / positive regulation of GTPase activity / nervous system development / postsynaptic density / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / neuron projection / glutamatergic synapse / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / protein phosphorylation / perinuclear region of cytoplasm / enzyme binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / 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 ...Rho GDP/GTP exchange factor Kalirin/TRIO / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / 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 repeats / Spectrin/alpha-actinin / RhoGEF domain / Dbl homology (DH) domain superfamily / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain / Fibronectin type III domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Fibronectin type 3 domain / Immunoglobulin C-2 Type / Immunoglobulin subtype 2 / Fibronectin type-III domain profile. / SH3 domain / Fibronectin type III / Fibronectin type III superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinases ATP-binding region signature. / Protein kinase, ATP binding site / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, matrix relaxation
Model detailsLowest total energy, model 121
AuthorsGorbatyuk, V.Y. / Schiller, M.R. / Hoch, J.C.
CitationJournal: To be Published
Title: The solution NMR structure of the first Dbl domain of RhoGEF Kalirin.
Authors: Gorbatyuk, V.Y. / Schiller, M.R. / Hoch, J.C.
History
DepositionDec 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _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: Kalirin


Theoretical massNumber of molelcules
Total (without water)21,9951
Polymers21,9951
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)15 / 100Total energy
RepresentativeModel #1lowest total energy

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Components

#1: Protein Kalirin / / Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine kinase with Dbl- ...Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine kinase with Dbl- and pleckstrin homology domain / PAM COOH-terminal interactor protein 10 / P-CIP10


Mass: 21995.221 Da / Num. of mol.: 1 / Fragment: DH 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kalrn, Duo, Hapip / Organ: brain / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P97924, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: N-terminal Kalirin DBL-homology domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1223D 1H-15N NOESY
131aroChsqc (H[C[caro]])
1422D 1H-15N HSQC/HMQC
1513D 1H-13C NOESY
1612D 1H-13C HSQC/HMQC
1714dCNnoesy (H[C] H[N].NOESY)
1812D 1H-15N HSQC/HMQC
1913D CBCA(CO)NH
11013D HN(CA)CB
11113D HNCO
11213D HN(CA)CO
11313D HNCA
11413D C(CO)NH
11513D (H)CCH-COSY
11613D (H)CCH-TOCSY
11713D HBHA(CO)NH
11823D HNHA
11923D NhsqcnoesyNhsqc

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] KalDH1, 50.0 mM Hepes, 90% H2O/10% D2O90% H2O/10% D2O
20.56 mM [U-100% 15N] KalDH1, 50.00 mM Hepes, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMKalDH1-1[U-100% 13C; U-100% 15N]1
50.0 mMHepes-21
0.56 mMKalDH1-3[U-100% 15N]2
50.00 mMHepes-42
Sample conditionsIonic strength: 0.05 / pH: 6.80 / Pressure: 1.00 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityInovaVarianUnityInova6001
Varian UnityInovaVarianUnityInova5002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Nilges M., et alstructure solution
CcpNmr Analysis1CCPNdata analysis
CcpNmr Analysis2.1CCPNdata analysis
CYANA2.1P. Guntertgeometry optimization
DANGLE1.1CCPNprocessing
NMRDrawF. Delaglio, et aldata analysis
NMRDrawF. Delaglio, et alprocessing
NMRPipeF. Delaglio, et alprocessing
SparkyT. D. Goddard and D. G. Knellerchemical shift assignment
SparkyT. D. Goddard and D. G. Knellerdata analysis
ARIA2.2Nilges M., et alrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, matrix relaxation
Software ordinal: 1
NMR representativeSelection criteria: lowest total energy
NMR ensembleConformer selection criteria: Total energy / Conformers calculated total number: 100 / Conformers submitted total number: 15

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