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- PDB-2o13: Solution structure of the C-terminal LIM domain of MLP/CRP3 -

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Basic information

Entry
Database: PDB / ID: 2o13
TitleSolution structure of the C-terminal LIM domain of MLP/CRP3
ComponentsMuscle LIM protein
KeywordsMETAL BINDING PROTEIN / LIM domain / zinc binding / CRP / MLP
Function / homology
Function and homology information


positive regulation of actin filament severing / negative regulation of actin filament severing / muscle tissue development / phospholipase C/protein kinase C signal transduction / T-tubule organization / establishment of protein localization to organelle / telethonin binding / detection of muscle stretch / cardiac myofibril assembly / regulation of the force of heart contraction ...positive regulation of actin filament severing / negative regulation of actin filament severing / muscle tissue development / phospholipase C/protein kinase C signal transduction / T-tubule organization / establishment of protein localization to organelle / telethonin binding / detection of muscle stretch / cardiac myofibril assembly / regulation of the force of heart contraction / negative regulation of myoblast differentiation / cardiac muscle hypertrophy / actinin binding / cardiac muscle tissue development / structural constituent of muscle / sarcomere organization / muscle cell cellular homeostasis / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / skeletal muscle tissue development / cardiac muscle contraction / Z disc / intracellular calcium ion homeostasis / insulin receptor signaling pathway / glucose homeostasis / actin binding / cytoskeleton / inflammatory response / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cysteine Rich Protein / Cysteine Rich Protein / 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. / Ribbon / Mainly Beta
Similarity search - Domain/homology
Cysteine and glycine-rich protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSchallus, T. / Muhle-Goll, C. / Edlich, C.
CitationJournal: To be Published
Title: Structure of the muscular LIM protein MLP and its interaction with Actinin
Authors: Schallus, T. / Stier, G. / Feher, K. / Muhle-Goll, C.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: 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: Muscle LIM protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5543
Polymers6,4241
Non-polymers1312
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 Muscle LIM protein / Cysteine and glycine-rich protein 3 / Cysteine-rich protein 3 / CRP3 / LIM domain protein / cardiac


Mass: 6423.557 Da / Num. of mol.: 1 / Fragment: LIM zinc-binding domain 2, residues 119-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSRP3, CLP, MLP / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 pLysS / References: UniProt: P50461
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 1.2mM C-terminal LIM domain, 20mM phosphate buffer K, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150mM KCl / pH: 6.8 / Pressure: ambient / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: zinc coordination fixed by explicit bonds and angles
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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