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- PDB-5k6p: The NMR structure of the m domain tri-helix bundle and C2 of huma... -

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Basic information

Entry
Database: PDB / ID: 5k6p
TitleThe NMR structure of the m domain tri-helix bundle and C2 of human cardiac Myosin Binding Protein C
ComponentsMyosin-binding protein C, cardiac-type
KeywordsCONTRACTILE PROTEIN / immunoglobulin
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 / Striated Muscle Contraction / positive regulation of ATP-dependent activity / 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 / Striated Muscle Contraction / positive regulation of ATP-dependent activity / A band / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / myosin binding / myosin heavy chain binding / ATPase activator activity / heart morphogenesis / titin binding / cardiac muscle contraction / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Myosin-binding protein C, cardiac-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsMichie, K.A. / Kwan, A.H. / Tung, C.S. / Guss, J.M. / Trewhella, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP120103841 Australia
CitationJournal: Structure / Year: 2016
Title: A Highly Conserved Yet Flexible Linker Is Part of a Polymorphic Protein-Binding Domain in Myosin-Binding Protein C.
Authors: Michie, K.A. / Kwan, A.H. / Tung, C.S. / Guss, J.M. / Trewhella, J.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary
Category: citation / entity ...citation / entity / pdbx_nmr_ensemble / pdbx_struct_assembly_auth_evidence
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_nmr_ensemble.conformer_selection_criteria
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,4981
Polymers15,4981
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9170 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy
DetailsMonomer as determined by gel filtration and SAXS

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Components

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


Mass: 15497.698 Da / Num. of mol.: 1 / Fragment: residues 319-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: heart / Gene: MYBPC3 / Plasmid: pETM
Details (production host): N-terminal hexahis tag and PreScission protease cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q14896

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
122isotropic23D HN(CA)CB
142isotropic13D HNCO
113isotropic22D 1H-15N HSQC
1163isotropic22D 1H-13C HSQC
133isotropic2HCC(CO)NH TOCSY
183isotropic2CC(CO)NH-TOCSY
173isotropic23D HBHA(CO)NH
193isotropic23D CBCA(CO)NH
1124isotropic23D 1H-15N NOESY
1104isotropic23D 13C NOESY aromatic
164isotropic23D (H)CCH-TOCSY
1204isotropic23D (H)CCH-TOCSY
1155isotropic22D (HB)CB(CGCD)HD
155isotropic12D (HB)CB(CGCDCE)HE
1135isotropic23D 13C NOESY aliphatic
1116isotropic22D 1H-13C HSQC aromatic
1146isotropic23D HCC TOCSY aromatic
1196isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution2412 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 2 mM TCEP, 1 mM Na azide, 10 mM DSS, 95% H2O/5% D2O15N_13C_sample195% H2O/5% D2O
solution3920 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 2 mM TCEP, 1 mM Na azide, 10 mM DSS, 95% H2O/5% D2O15N_13C_sample295% H2O/5% D2Ohigh concentration sample
solution4550 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 1 mM Na azide, 2 mM TCEP, 10 mM DSS, 95% H2O/5% D2O15N_13C_sample395% H2O/5% D2Odilution of sample 2
solution5500 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 2 mM TCEP, 1 mM Na azide, 10 mM DSS, 99% D2O15N_13C_sample499% D2O15N_13C_sample3, freeze dried (part 1 of 2) and re-suspended in 99% D2O.
solution6800 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 2 mM TCEP, 1 mM Na azide, 10 mM DSS, 99% D2O15N_13C_sample599% D2O15N_13C_sample3 was freeze dried (part 2 of 2) and re-suspended in 99% D2O.
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
412 uMhuman cMyBP-C (319-451)[U-99% 13C; U-99% 15N]2
10 mMMESnatural abundance2
1 mMCaCl2natural abundance2
50 mMNaClnatural abundance2
2 mMTCEPnatural abundance2
1 mMNa azidenatural abundance2
10 mMDSSnatural abundance2
920 uMhuman cMyBP-C (319-451)[U-99% 13C; U-99% 15N]3
10 mMMESnatural abundance3
1 mMCaCl2natural abundance3
50 mMNaClnatural abundance3
2 mMTCEPnatural abundance3
1 mMNa azidenatural abundance3
10 mMDSSnatural abundance3
550 uMhuman cMyBP-C (319-451)[U-99% 13C; U-99% 15N]4
10 mMMESnatural abundance4
1 mMCaCl2natural abundance4
50 mMNaClnatural abundance4
1 mMNa azidenatural abundance4
2 mMTCEPnatural abundance4
10 mMDSSnatural abundance4
500 uMhuman cMyBP-C (319-451)[U-99% 13C; U-99% 15N]5
10 mMMESnatural abundance5
1 mMCaCl2natural abundance5
50 mMNaClnatural abundance5
2 mMTCEPnatural abundance5
1 mMNa azidenatural abundance5
10 mMDSSnatural abundance5
800 uMhuman cMyBP-C (319-451)[U-99% 13C; U-99% 15N]6
10 mMMESnatural abundance6
1 mMCaCl2natural abundance6
50 mMNaClnatural abundance6
2 mMTCEPnatural abundance6
1 mMNa azidenatural abundance6
10 mMDSSnatural abundance6
Sample conditionsIonic strength: 50 mM / Label: std_condition / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 2
Details: torsion angle dynamics, water refinement was carried out using the lowest 50 energy structures from CYANA
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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