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- PDB-6mg9: Human Obscurin Ig57 Domain -

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Basic information

Entry
Database: PDB / ID: 6mg9
TitleHuman Obscurin Ig57 Domain
ComponentsObscurin
KeywordsSTRUCTURAL PROTEIN / obscurin / ig domain / wlc
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 / sarcomere organization / ankyrin binding ...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 / sarcomere organization / ankyrin binding / myofibril / 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 / calmodulin binding / non-specific serine/threonine protein kinase / 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. / Pleckstrin homology domain / Fibronectin type III 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 / 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 / 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 / simulated annealing
AuthorsWright, N.T. / Whitley, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1757874 United States
National Science Foundation (NSF, United States)MCB-160724 United States
CitationJournal: Protein Sci. / Year: 2019
Title: Obscurin is a semi-flexible molecule in solution.
Authors: Whitley, J.A. / Ex-Willey, A.M. / Marzolf, D.R. / Ackermann, M.A. / Tongen, A.L. / Kokhan, O. / Wright, N.T.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model

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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)11,1121
Polymers11,1121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size Exclusion G75
TypeNameSymmetry operationNumber
identity operation1_5551
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: 11112.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OBSCN, KIAA1556, KIAA1639 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q5VST9, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
132isotropic13D 1H-13C NOESY
142isotropic13D CBCA(CO)NH
152isotropic13D C(CO)NH
162isotropic13D H(CCO)NH
172isotropic13D HN(CA)CB
182isotropic13D HN(CO)CA
192isotropic13D HNCO
1101isotropic13D 1H-15N TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM TRIS, 1 mM DTT, 50 mM sodium chloride, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution220 mM TRIS, 1 mM DTT, 50 mM sodium chloride, 90% H2O/10% D2Odouble_labelled_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRISnatural abundance1
1 mMDTTnatural abundance1
50 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance2
1 mMDTTnatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 283 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
TopSpinBruker Biospincollection
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
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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