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- PDB-2n56: Ig59 domain of human obscurin A -

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Basic information

Entry
Database: PDB / ID: 2n56
TitleIg59 domain of human obscurin A
ComponentsObscurin
KeywordsPROTEIN BINDING / Ig-like / I-set
Function / homology
Function and homology information


protein localization to M-band / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / M band / phosphatidylinositol-4-phosphate binding / regulation of small GTPase mediated signal transduction / structural constituent of muscle / ankyrin binding / myofibril ...protein localization to M-band / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / M band / phosphatidylinositol-4-phosphate binding / regulation of small GTPase mediated signal transduction / structural constituent of muscle / ankyrin binding / myofibril / sarcomere organization / NRAGE signals death through JNK / RHOQ GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / RHOA GTPase cycle / titin binding / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / sarcolemma / Z disc / G alpha (12/13) signalling events / nuclear body / non-specific serine/threonine protein kinase / calmodulin binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Obscurin, SH3 domain / IQ calmodulin-binding motif / 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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site ...Obscurin, SH3 domain / IQ calmodulin-binding motif / 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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Fibronectin type III domain / Pleckstrin homology domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Tyrosine-protein kinase, active site / 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 / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model1
AuthorsWright, N.T. / Caldwell, T.A.
CitationJournal: To be Published
Title: Identification and characterization of disease-causing obscurin mutations
Authors: Wright, N.T. / Caldwell, T.A.
History
DepositionJul 8, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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: Obscurin


Theoretical massNumber of molelcules
Total (without water)11,2211
Polymers11,2211
Non-polymers00
Water00
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 least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Obscurin / Obscurin-RhoGEF / Obscurin-myosin light chain kinase / Obscurin-MLCK


Mass: 11220.501 Da / Num. of mol.: 1 / Fragment: UNP residues 4430-4524
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OBSCN, KIAA1556, KIAA1639 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5VST9, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Ig59 (4430-4524) of human obscurin
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D H(CCO)NH
1613D C(CO)NH
1713D HNCO
1813D HCACO
1912D 1H-15N HSQC

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Sample preparation

DetailsContents: 1.5 mM [U-100% 13C; U-100% 15N] protein, 10 % [U-100% 2H] D2O, 350 uM sodium azide, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMentity-1[U-100% 13C; U-100% 15N]1
10 %D2O-2[U-100% 2H]1
350 uMsodium azide-31
20 mMTRIS-41
50 mMsodium chloride-51
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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