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- PDB-2jv9: The Solution Structure of Calponin Homology Domain from Smootheli... -

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Basic information

Entry
Database: PDB / ID: 2jv9
TitleThe Solution Structure of Calponin Homology Domain from Smoothelin-like 1
ComponentsSmoothelin-like 1
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING / CH-domain / Smoothelin / Smoothelin-like 1 / Calponin / Calponin homology domain
Function / homology
Function and homology information


myosin phosphatase regulator activity / CH domain binding / muscle organ morphogenesis / contractile muscle fiber / protein phosphatase 1 binding / vasoconstriction / M band / I band / protein phosphatase inhibitor activity / microtubule organizing center ...myosin phosphatase regulator activity / CH domain binding / muscle organ morphogenesis / contractile muscle fiber / protein phosphatase 1 binding / vasoconstriction / M band / I band / protein phosphatase inhibitor activity / microtubule organizing center / tropomyosin binding / filamentous actin / positive regulation of vasoconstriction / response to activity / : / disordered domain specific binding / actin cytoskeleton organization / calmodulin binding / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / nucleus / cytoplasm
Similarity search - Function
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
Smoothelin-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsIshida, H. / Vogel, H.J. / MacDonald, J.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Solution Structure of the Calponin Homology (CH) Domain from the Smoothelin-like 1 Protein: A UNIQUE APOCALMODULIN-BINDING MODE AND THE POSSIBLE ROLE OF THE C-TERMINAL TYPE-2 CH-DOMAIN IN SMOOTH MUSCLE RELAXATION.
Authors: Ishida, H. / Borman, M.A. / Ostrander, J. / Vogel, H.J. / Macdonald, J.A.
History
DepositionSep 12, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Smoothelin-like 1


Theoretical massNumber of molelcules
Total (without water)13,6941
Polymers13,6941
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)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Smoothelin-like 1 / Novel protein / 1110030K22Rik


Mass: 13693.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smtnl1, RP23-399J8.5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q99LM3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CA)CO
1522D 1H-15N HSQC
1612D 1H-13C HSQC
1732D 1H-1H NOESY
1813D H(CCO)NH
1913D C(CO)NH
11013D HBHA(CO)NH
11113D 13C-edited NOESY
11223D 15N-edited NOESY
21322D IPAP-1H-15N HSQC
21442D IPAP-1H-15N HSQC
11512D (HB)CB(CGCDCE)HE
11612D (HB)CB(CGCD)HD

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0 mM [U-99% 13C; U-99% 15N] smoothelin-like 1, 1 mM sodium phosphate, 0.5 mM DSS, 10 mM [U-2H] DTT, 0.03 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1.0 mM [U-99% 15N] smoothelin-like 1, 1 mM sodium phosphate, 0.5 mM DSS, 10 mM [U-2H] DTT, 0.03 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.5-1.0 mM smoothelin-like 1, 1 mM sodium phosphate, 0.5 mM DSS, 10 mM [U-2H] DTT, 0.03 % sodium azide, 100% D2O100% D2O
40.5-1.0 mM [U-99% 15N] smoothelin-like 1, 10 mg/mL Pf1 phage, 0.05 mM DSS, 10 mM [U-2H] DTT, 0.03 % sodium azide, 300 mM potassium chloride, 20 mM Bis-Tris, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMsmoothelin-like 1[U-99% 13C; U-99% 15N]1
1 mMsodium phosphate1
0.5 mMDSS1
10 mMDTT[U-2H]1
0.03 %sodium azide1
0.5 mMsmoothelin-like 1[U-99% 15N]2
1 mMsodium phosphate2
0.5 mMDSS2
10 mMDTT[U-2H]2
0.03 %sodium azide2
0.5 mMsmoothelin-like 13
1 mMsodium phosphate3
0.5 mMDSS3
10 mMDTT[U-2H]3
0.03 %sodium azide3
0.5 mMsmoothelin-like 1[U-99% 15N]4
10 mg/mLPf1 phage4
0.05 mMDSS4
10 mMDTT[U-2H]4
0.03 %sodium azide4
300 mMpotassium chloride4
20 mMBis-Tris4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 7.0 ambient 293 K
2300 7.0 ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, P. et al.structure solution
X-PLOR NIH2.14Schwieters, C.D. et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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