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- PDB-2dk9: Solution structure of Calponin Homology domain of Human MICAL-1 -

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Basic information

Entry
Database: PDB / ID: 2dk9
TitleSolution structure of Calponin Homology domain of Human MICAL-1
ComponentsNEDD9-interacting protein with calponin homology and LIM domains
KeywordsSIGNALING PROTEIN / helix
Function / homology
Function and homology information


hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / actin filament depolymerization ...hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / actin filament depolymerization / intermediate filament / intercellular bridge / actin filament bundle assembly / cytoskeleton organization / negative regulation of protein phosphorylation / FAD binding / monooxygenase activity / actin filament / SH3 domain binding / small GTPase binding / actin filament binding / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / actin binding / midbody / endosome membrane / negative regulation of apoptotic process / protein kinase binding / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / FAD-binding domain / FAD binding domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / FAD/NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
[F-actin]-monooxygenase MICAL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsSun, H. / Dai, H. / Zhang, J. / Xiong, S. / Wu, J. / Shi, Y.
CitationJournal: J.Biomol.Nmr / Year: 2006
Title: Solution structure of calponin homology domain of Human MICAL-1
Authors: Sun, H. / Dai, H. / Zhang, J. / Jin, X. / Xiong, S. / Xu, J. / Wu, J. / Shi, Y.
History
DepositionApr 7, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 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: NEDD9-interacting protein with calponin homology and LIM domains


Theoretical massNumber of molelcules
Total (without water)12,5791
Polymers12,5791
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NEDD9-interacting protein with calponin homology and LIM domains / Molecule interacting with CasL protein 1 / MICAL-1


Mass: 12579.180 Da / Num. of mol.: 1 / Fragment: Calponin Homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICAL1, MICAL, NICAL / Plasmid: p28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8TDZ2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D HNCO, HN(CA)CO, CBCA(CO)NH, CBCANH, C(CO)NH-TOCSY, H(CCO)NH-TOCSY, HBHA(CBCACO)NH,3D 15N-separted NOESY
1333D (H)CCH-TOCSY, (H)CCH-COSY, 13C-separted NOESY
1441H-coupled IPAP {15N, 1H}-HSQC
NMR detailsText: This structure was determined using standard 3D homonuclear techniques and residual dipolar couplings data

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM MICAL_1 CH U-15N,13C; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM MICAL_1 CH U-15N; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
31.5mM MICAL_1 CH U-15N,13C; 50mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O
41.5mM MICAL_1 CH U-15N; 50mM phosphate buffer, 50mM NaCl; 17 mg/mL Pf1 filamentous phage; 90% H2O, 10% D2O17 mg/mL Pf1 filamentous phage; 90% H2O, 10% D2O
Sample conditionsIonic strength: 50mM phosphate buffer, 50mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1brukercollection
NMRPipe2.3Delaglioprocessing
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
MOLMOL2k.2Koradistructure solution
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 2042 restraints, 1746 are NOE-derived distance constraints, 140 dihedral angle restraints,82 distance restraints from hydrogen bonds,74 residual ...Details: the structures are based on a total of 2042 restraints, 1746 are NOE-derived distance constraints, 140 dihedral angle restraints,82 distance restraints from hydrogen bonds,74 residual dipolar couplings restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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