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- PDB-1pd6: The NMR structure of domain C2 of human cardiac Myosin Binding Pr... -

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Basic information

Entry
Database: PDB / ID: 1pd6
TitleThe NMR structure of domain C2 of human cardiac Myosin Binding Protein C
ComponentsMyosin-binding protein C, cardiac-type, Domain C2
KeywordsSTRUCTURAL PROTEIN / Ig domain
Function / homology
Function and homology information


C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / cardiac myofibril / regulation of striated muscle contraction / positive regulation of ATP-dependent activity / Striated Muscle Contraction / A band / ventricular cardiac muscle tissue morphogenesis / structural constituent of muscle ...C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / cardiac myofibril / regulation of striated muscle contraction / positive regulation of ATP-dependent activity / Striated Muscle Contraction / A band / ventricular cardiac muscle tissue morphogenesis / structural constituent of muscle / myosin binding / sarcomere organization / myosin heavy chain binding / ATPase activator activity / heart morphogenesis / cardiac muscle contraction / titin binding / sarcomere / actin binding / cell adhesion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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 / Fibronectin type-III domain profile. / Fibronectin type III ...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 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myosin-binding protein C, cardiac-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / we have used ARIA protocols
AuthorsAbabou, A. / Gautel, M. / Pfuhl, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Dissecting the N-terminal myosin binding site of human cardiac myosin-binding protein C. Structure and myosin binding of domain C2
Authors: Ababou, A. / Gautel, M. / Pfuhl, M.
History
DepositionMay 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Myosin-binding protein C, cardiac-type, Domain C2


Theoretical massNumber of molelcules
Total (without water)11,7651
Polymers11,7651
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)28 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Myosin-binding protein C, cardiac-type, Domain C2 / cardiac myosin-binding protein C / Cardiac MyBP-C / protein C / cardiac


Mass: 11765.365 Da / Num. of mol.: 1 / Fragment: Domain C2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: muscle / Gene: MYBPC3 / Organ: heart / Plasmid: pET-8a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: Q14896

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY
3333D 13C-separated NOESY
NMR detailsText: Further NMR experiments could be found in the BMRB accession number 5591

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75mM C2; 15N; 20mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
20.75mM C2; 15N, 13C; 20mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
30.75mM C2; 15N, 13C; 20mM phosphate buffer; 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 7.0 ambient 298 K
20.1 7.0 ambient 298 K
37.0 7.0 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE6002
Varian UnityINOVAVarianUnityINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
ANSIG3.3Kraulis, J.data analysis
ARIA1.1Linge, J., O'Donoghue, S., Nilges, M.structure solution
NMRPipe290302Delaglio, F., Grzesiek, S., Zhu, G., Vuister, G.W., Pfeifer, J., Bax, A.processing
Azara2.6Boucher, W.data analysis
ARIA1.1Linge, J., O'Donoghue, S., Nilges, M.refinement
RefinementMethod: we have used ARIA protocols / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 28

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