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- PDB-1wyp: Solution structure of the CH domain of human Calponin 1 -

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Basic information

Entry
Database: PDB / ID: 1wyp
TitleSolution structure of the CH domain of human Calponin 1
ComponentsCalponin 1
KeywordsSTRUCTURAL PROTEIN / CH domain / F-actin binding / all-alpha / structural genomics / NPPSFA / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of smooth muscle contraction / actomyosin structure organization / negative regulation of vascular associated smooth muscle cell proliferation / actin binding / cytoskeleton / calmodulin binding / focal adhesion
Similarity search - Function
Calponin/LIMCH1 / Calponin repeat / Calponin family repeat / Calponin-like repeat signature. / Calponin-like repeat profile. / Smooth muscle protein/calponin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / Calponin homology (CH) domain ...Calponin/LIMCH1 / Calponin repeat / Calponin family repeat / Calponin-like repeat signature. / Calponin-like repeat profile. / Smooth muscle protein/calponin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the CH domain of human Calponin 1
Authors: Tomizawa, T. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionFeb 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _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: Calponin 1


Theoretical massNumber of molelcules
Total (without water)14,9921
Polymers14,9921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Calponin 1 / / Calponin H1 / smooth muscle / Basic calponin


Mass: 14991.778 Da / Num. of mol.: 1 / Fragment: CH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: CNN1 / Plasmid: P040621-01 / References: UniProt: P51911

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.10mM CH domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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