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- PDB-1v1c: Solution Structure of the SH3 domain of Obscurin -

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Basic information

Entry
Database: PDB / ID: 1v1c
TitleSolution Structure of the SH3 domain of Obscurin
ComponentsOBSCURIN
KeywordsSH3-DOMAIN / MUSCLE / SARCOMERE / ADAPTER / MYOGENESIS
Function / homology
Function and homology information


: / protein localization to M-band / phosphatidylinositol-5-phosphate binding / multicellular organism development / 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 ...: / protein localization to M-band / phosphatidylinositol-5-phosphate binding / multicellular organism development / 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 / sarcomere organization / 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 / non-specific serine/threonine protein kinase / calmodulin binding / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / 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 / SH3 Domains / 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 / SH3 type barrels. / 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 / 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 speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPfuhl, M. / Gautel, M.
CitationJournal: To be Published
Title: Solution Structure of the SH3 Domain of Obscurin
Authors: Pfuhl, M. / Gautel, M.
History
DepositionApr 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _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)8,0261
Polymers8,0261
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 / 200LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein OBSCURIN /


Mass: 8026.125 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN RESIDUES 5601-5668
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLESkeletal muscle / Cell: MYOCYTE / Organ: HEART / Plasmid: PET8C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q96AA2, UniProt: Q5VST9*PLUS
Sequence detailsTHE FIRST THREE RESIDUES IN THE SEQRES RECORDS BELOW ARE THE REMANENTS OF A TEV CLEAVED HIS TAG AND ...THE FIRST THREE RESIDUES IN THE SEQRES RECORDS BELOW ARE THE REMANENTS OF A TEV CLEAVED HIS TAG AND DO NOT FORM PART OF THE OBSCURIN SH3 DOMAIN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-RESOLVED NOESY-HSQC
1213D 13C RESOLVED NOESY-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED OBSH3

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Sample preparation

Sample conditionsIonic strength: 200 mM / pH: 5.76 / Pressure: 1 atm / 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
NameVersionDeveloperClassification
CNS1.1BRUNGER ET.AL.refinement
CNS/ARIAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STANDARD ARIA SIMULATED ANNEALING PROTOCOL ACCORDING TO NILGES. ALL DEFAULT PARAMETERS COMING WITH VERSION 1.2 WERE USED APART FROM A NUMBER OF 200 STRUCTURES CALCULATED IN ITERATION 8 OF ...Details: STANDARD ARIA SIMULATED ANNEALING PROTOCOL ACCORDING TO NILGES. ALL DEFAULT PARAMETERS COMING WITH VERSION 1.2 WERE USED APART FROM A NUMBER OF 200 STRUCTURES CALCULATED IN ITERATION 8 OF WHICH 20 WHERE SELECTED. NO WATER REFINEMENT WAS USED.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 200 / Conformers submitted total number: 20

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