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- PDB-2avg: NMR structure of cC1 domain from Human Cardiac Myosin Binding Pro... -

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Basic information

Entry
Database: PDB / ID: 2avg
TitleNMR structure of cC1 domain from Human Cardiac Myosin Binding Protein C
ComponentsMyosin-binding protein C, cardiac-type
KeywordsSTRUCTURAL PROTEIN / Human Cardiac MyBP-C
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 / simulated annealing using ARIA program
AuthorsAbabou, A. / Gautel, M. / Pfuhl, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Myosin binding protein C positioned to play a key role in regulation of muscle contraction: structure and interactions of domain C1.
Authors: Ababou, A. / Rostkova, E. / Mistry, S. / Le Masurier, C. / Gautel, M. / Pfuhl, M.
History
DepositionAug 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-binding protein C, cardiac-type


Theoretical massNumber of molelcules
Total (without water)13,4871
Polymers13,4871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)29 / 40no NOE violation > 0.5 A
RepresentativeModel #1lowest energy

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Components

#1: Protein Myosin-binding protein C, cardiac-type / Cardiac MyBP-C / C-protein / cardiac muscle isoform


Mass: 13487.283 Da / Num. of mol.: 1 / Fragment: cC1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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
1223D 13C-separated NOESY
1333D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM cC1 U-15N; 20mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
20.8mM cC1 U-15N, 13C; 20mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
30.8mM cC1 U-15N, 13C; 20mM phosphate buffer; 100% D2O100% D2O
Sample conditionsIonic strength: 0.1M / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian UNITYINOVAVarianUNITYINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe290302Delaglio F.processing
ANSIG3.3Kraulis P.data analysis
ARIA1.2Linge J. & Nilges M.structure solution
Azara2.6Boucher W.data analysis
ARIA1.2Linge J. & Nilges M.refinement
RefinementMethod: simulated annealing using ARIA program / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: no NOE violation > 0.5 A / Conformers calculated total number: 40 / Conformers submitted total number: 29

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