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- PDB-2mq3: NMR structure of the c3 domain of human cardiac myosin binding pr... -

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Basic information

Entry
Database: PDB / ID: 2mq3
TitleNMR structure of the c3 domain of human cardiac myosin binding protein-c with a hypertrophic cardiomyopathy-related mutation R502W.
ComponentsMyosin-binding protein C, cardiac-type
KeywordsCONTRACTILE PROTEIN / cardiac myosin binding protein C / C3 domain / Ig-like / hypertrophic cardiomyopathy
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 / torsion angle dynamics
Model detailslowest energy, model1
AuthorsZhang, X. / De, S. / Mcintosh, L.P. / Paetzel, M.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Characterization of the C3 Domain of Cardiac Myosin Binding Protein C and Its Hypertrophic Cardiomyopathy-Related R502W Mutant.
Authors: Zhang, X.L. / De, S. / McIntosh, L.P. / Paetzel, M.
History
DepositionJun 12, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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)10,8561
Polymers10,8561
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)10 / 10structures with the lowest energy
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: 10856.336 Da / Num. of mol.: 1 / Fragment: unp residues 453-543 / Mutation: R502W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYBPC3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q14896

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY

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Sample preparation

DetailsContents: 50 mM sodium phosphate, 100 mM sodium chloride, 0.8 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
100 mMsodium chloride-21
0.8 mMentity-3[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 0.4 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1412 / NOE intraresidue total count: 356 / NOE long range total count: 520 / NOE medium range total count: 152 / NOE sequential total count: 384
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Maximum upper distance constraint violation: 0.06 Å

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