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- PDB-2lhu: Structural Insight into the Unique Cardiac Myosin Binding Protein... -

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Basic information

Entry
Database: PDB / ID: 2lhu
TitleStructural Insight into the Unique Cardiac Myosin Binding Protein-C Motif: A Partially Folded Domain
ComponentsMybpc3 protein
KeywordsSTRUCTURAL PROTEIN / CARDIAC
Function / homology
Function and homology information


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
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR
Model detailslowest energy, model 1
AuthorsHowarth, J.W. / Rosevear, P.R. / Ramisetti, S. / Nolan, K. / Sadayappan, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Insight into Unique Cardiac Myosin-binding Protein-C Motif: A PARTIALLY FOLDED DOMAIN.
Authors: Howarth, J.W. / Ramisetti, S. / Nolan, K. / Sadayappan, S. / Rosevear, P.R.
History
DepositionAug 18, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mybpc3 protein


Theoretical massNumber of molelcules
Total (without water)13,9981
Polymers13,9981
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)20 / 5000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mybpc3 protein


Mass: 13997.658 Da / Num. of mol.: 1 / Fragment: UNP residues 255-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mybpc3 / Production host: Escherichia coli (E. coli) / References: UniProt: A9JR55

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HCACO
1613D C(CO)NH
1713D HBHA(CO)NH
1813D 1H-15N NOESY
1913D 1H-15N TOCSY

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Sample preparation

DetailsContents: 1.0 mM [U-13C; U-15N] myosin binding protein-C (255-357), 20.0 mM [U-2H] TRIS, 50.0 mM sodium chloride, 2.0 mM TCEP, 1.0 mM EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMmyosin binding protein-C (255-357)-1[U-13C; U-15N]1
20.0 mMTRIS-2[U-2H]1
50.0 mMsodium chloride-31
2.0 mMTCEP-41
1.0 mMEDTA-51
Sample conditionsIonic strength: 0.05 / pH: 6.8 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
SparkyGoddardchemical shift assignment
CS-ROSETTAYang Shen, Robert Vernon, David Baker and Ad Baxstructure solution
CS-ROSETTAYang Shen, Robert Vernon, David Baker and Ad Baxrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 5000 / Conformers submitted total number: 20

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