PDB-2k3s: HADDOCK-derived structure of the CH-domain of the smoothelin-like...

Basic information

• Entry: Database: PDB / ID: 2k3s
• Title: HADDOCK-derived structure of the CH-domain of the smoothelin-like 1 complexed with the C-domain of apocalmodulin

Components

• Calmodulin
• Smoothelin-like protein 1

• Keywords: PROTEIN BINDING / apocalmodulin complex / calponin homology domain / smoothelin-like 1 / HADDOCK model / CH-domain / Coiled coil / Acetylation / Calcium / Methylation

Function / homology

Function:

myosin phosphatase regulator activity / CH domain binding / muscle organ morphogenesis / contractile muscle fiber / protein phosphatase 1 binding / vasoconstriction / M band / I band / microtubule organizing center / protein phosphatase inhibitor activity / tropomyosin binding / filamentous actin / positive regulation of vasoconstriction / response to activity / : / disordered domain specific binding / actin cytoskeleton organization / calmodulin binding / response to xenobiotic stimulus / signaling receptor binding / negative regulation of DNA-templated transcription / calcium ion binding / nucleus / cytoplasm

Domain/homology:

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. / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha

Component:

Calmodulin-1 / Calmodulin-2 B / Smoothelin-like protein 1

• Biological species: Mus musculus (house mouse); Xenopus laevis (African clawed frog)
• Method: SOLUTION NMR / HADDOCK docking calculation
• Authors: Ishida, H. / Borman, M.A. / Ostrander, J. / Vogel, H.J. / MacDonald, J.A.
• Citation: Journal: 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

Deposition	May 15, 2008	Deposition site: BMRB / Processing site: RCSB
Revision 1.0	May 27, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Mar 16, 2022	Group: Data collection / Database references / Derived calculations Category: database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

Assembly

Deposited unit

A: Smoothelin-like protein 1

B: Calmodulin

Summary:

• 21.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	21,431	2
Polymers	21,431	2
Non-polymers	0	0
Water	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	15 / 1000	structures with the lowest energy
Representative	Model #1	lowest energy

Components

#1: Protein

A Smoothelin-like protein 1

Details:

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 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99LM3

#2: Protein

B Calmodulin / / CaM

Details:

Mass: 7737.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: calm1 / Plasmid: Ptnco12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62155, UniProt: P0DP33*PLUS

Experimental details

Experiment

• Experiment: Method: SOLUTION NMR
• NMR experiment: Type: 2D 1H-15N HSQC

Sample preparation

Details

Solution-ID	Contents	Solvent system
1	0.5 mM [U-100% 15N] entity_1, 0.6 mM calmodulin (full length), 20 mM Bis-Tris, 0.5 mM DSS, 10 mM [U-2H] DTT, 0.03 % sodium azide, 1 mM EDTA, 90% H2O/10% D2O	90% H2O/10% D2O
2	0.6 mM entity_1, 0.5 mM [U-100% 15N] calmodulin (full length), 20 mM Bis-Tris, 0.5 mM DSS, 10 mM [U-2H] DTT, 0.03 % sodium azide, 1 mM EDTA, 90% H2O/10% D2O	90% H2O/10% D2O

Sample

Conc. (mg/ml)	Component	Isotopic labeling	Solution-ID
0.5 mM	entity_1	[U-100% 15N]	1
0.6 mM	calmodulin (full length)		1
20 mM	Bis-Tris		1
0.5 mM	DSS		1
10 mM	DTT	[U-2H]	1
0.03 %	sodium azide		1
1 mM	EDTA		1
0.6 mM	entity_1		2
0.5 mM	calmodulin (full length)	[U-100% 15N]	2
20 mM	Bis-Tris		2
0.5 mM	DSS		2
10 mM	DTT	[U-2H]	2
0.03 %	sodium azide		2
1 mM	EDTA		2

• Sample conditions: Ionic strength: 0 / pH: 7.0 / Pressure: ambient / Temperature: 293 K

NMR measurement

• NMR spectrometer: Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

Processing

NMR software

Name	Version	Developer	Classification
HADDOCK	2	Dominguez, C. et al.	structure solution
HADDOCK	2	Dominguez, C. et al.	refinement

• Refinement: Method: HADDOCK docking calculation / Software ordinal: 1
• NMR representative: Selection criteria: lowest energy
• NMR ensemble: Conformer selection criteria: structures with the lowest energy; Conformers calculated total number: 1000 / Conformers submitted total number: 15