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- PDB-2k1m: 3D NMR structure of domain cC0 of cardiac myosin binding protein ... -

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Basic information

Entry
Database: PDB / ID: 2k1m
Title3D NMR structure of domain cC0 of cardiac myosin binding protein C (MyBPC)
ComponentsMyosin-binding protein C, cardiac-type
KeywordsSTRUCTURAL PROTEIN / Ig-I domain / Myosin Binding Protein C / Cardiac Muscle / Hypertrophic cardiomyopathy / Actin-binding / Cell adhesion / Disease mutation / Immunoglobulin domain / Muscle protein / Phosphoprotein / Polymorphism / Thick filament
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 / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis ...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 / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / myosin binding / 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. ...: / 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
AuthorsRatti, J. / Gautel, M. / Pfuhl, M.
CitationJournal: To be Published
Title: 3D NMR structure of domain cC0 of cardiac myosin binding protein C (MyBPC)
Authors: Ratti, J. / Gautel, M. / Pfuhl, M.
History
DepositionMar 10, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 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_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)10,0451
Polymers10,0451
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 / 100target function
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: 10045.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYBPC3 / Plasmid: pET-8C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: Q14896

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1222D 1H-15N HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CO)CA
1732D 1H-1H NOESY
1812D 1H-13C HSQC
1913D (H)CCH-TOCSY
11023D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-1.5 mM [U-95% 13C; U-95% 15N] cC0_MyBPC, 55.5 M [U-2H] D2O, 40 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21-1.5 mM [U-95% 15N] cC0_MyBPC, 55.5 M H2O, 40 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
31-1.5 mM cC0_MyBPC, 55.5 M H2O, 40 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMcC0_MyBPC[U-95% 13C; U-95% 15N]1
55.5 MD2O[U-2H]1
40 mMsodium phosphate1
50 mMsodium chloride1
2 mMDTT1
1 mMcC0_MyBPC[U-95% 15N]2
55.5 MH2O2
40 mMsodium phosphate2
50 mMsodium chloride2
2 mMDTT2
1 mMcC0_MyBPC3
55.5 MH2O3
40 mMsodium phosphate3
50 mMsodium chloride3
2 mMDTT3
Sample conditionsIonic strength: 185 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdihedral angles
CCPNMR-_analysis1.0 release 15Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Foghchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2066 / NOE intraresidue total count: 0 / NOE long range total count: 701 / NOE medium range total count: 87 / NOE sequential total count: 1278 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 90 / Protein psi angle constraints total count: 90
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 2.82 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.24 Å / Maximum torsion angle constraint violation: 4.23 ° / Maximum upper distance constraint violation: 0.32 Å
NMR ensemble rmsDistance rms dev: 0.4 Å / Distance rms dev error: 0.07 Å

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