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- PDB-2rq8: Solution NMR structure of titin I27 domain mutant -

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Basic information

Entry
Database: PDB / ID: 2rq8
TitleSolution NMR structure of titin I27 domain mutant
ComponentsTitin
KeywordsTRANSFERASE / Beta-sandwich / Immunoglobulin-like domain / Alternative splicing / ATP-binding / Calcium / Calmodulin-binding / Cardiomyopathy / Coiled coil / Cytoplasm / Disease mutation / Disulfide bond / Immunoglobulin domain / Isopeptide bond / Kelch repeat / Kinase / Limb-girdle muscular dystrophy / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / TPR repeat / Ubl conjugation / WD repeat
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / protein kinase regulator activity / cardiac muscle hypertrophy ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / protein kinase regulator activity / cardiac muscle hypertrophy / mitotic chromosome condensation / actinin binding / Striated Muscle Contraction / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / cardiac muscle contraction / striated muscle contraction / muscle contraction / protein kinase A signaling / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulins / 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 / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsYagawa, K. / Oguro, T. / Momose, T. / Kawano, S. / Sato, T. / Endo, T.
CitationJournal: Protein Sci. / Year: 2010
Title: Structural basis for unfolding pathway-dependent stability of proteins: Vectorial unfolding vs. global unfolding
Authors: Yagawa, K. / Yamano, K. / Oguro, T. / Maeda, M. / Sato, T. / Momose, T. / Kawano, S. / Endo, T.
History
DepositionMar 5, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin


Theoretical massNumber of molelcules
Total (without water)10,9301
Polymers10,9301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 10930.482 Da / Num. of mol.: 1 / Fragment: UNP residues 12677-12765 / Mutation: K3E, Y9P, T42A, A78T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8WZ42, 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-IDType
1112D 1H-1H NOESY
1223D 1H-15N NOESY
1333D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM TITIN I27 mutant, 50mM potassium phosphate buffer, 99.9% D2O99.9% D2O
21.0mM [U-15N] TITIN I27 mutant, 50mM potassium phosphate buffer, 90% H2O/10% D2O90% H2O/10% D2O
31.0mM [U-13C; U-15N] TITIN I27 mutant, 50mM potassium phosphate buffer, 99.9% D2O99.9% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMpotassium phosphate-11
1.0 mMpotassium phosphate-2[U-15N]2
1.0 mMpotassium phosphate-3[U-13C; U-15N]3
Sample conditionsIonic strength: 50mM POTASSIUM PHOSPHATE / pH: 7.4 / 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 softwareName: CYANA / Version: 2.1 / Developer: P.GUNTERT ET AL. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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