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- PDB-1y74: Solution Structure of mLin-2/mLin-7 L27 Domain Complex -

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Basic information

Entry
Database: PDB / ID: 1y74
TitleSolution Structure of mLin-2/mLin-7 L27 Domain Complex
Components
  • Peripheral plasma membrane protein CASK
  • lin 7 homolog b
KeywordsTRANSPORT PROTEIN / L27 domain / scaffold protein / protein assembly / cell polarity
Function / homology
Function and homology information


podocyte foot / RHO GTPases Activate Rhotekin and Rhophilins / Dopamine Neurotransmitter Release Cycle / protein localization to basolateral plasma membrane / Neurexins and neuroligins / negative regulation of cellular response to growth factor stimulus / L27 domain binding / MPP7-DLG1-LIN7 complex / maintenance of epithelial cell apical/basal polarity / neurexin family protein binding ...podocyte foot / RHO GTPases Activate Rhotekin and Rhophilins / Dopamine Neurotransmitter Release Cycle / protein localization to basolateral plasma membrane / Neurexins and neuroligins / negative regulation of cellular response to growth factor stimulus / L27 domain binding / MPP7-DLG1-LIN7 complex / maintenance of epithelial cell apical/basal polarity / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / positive regulation of dendritic spine morphogenesis / neurotransmitter secretion / apical dendrite / calcium ion import / ciliary membrane / transport vesicle membrane / regulation of synaptic vesicle exocytosis / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / exocytosis / basement membrane / bicellular tight junction / negative regulation of keratinocyte proliferation / synaptic membrane / establishment of localization in cell / protein localization to plasma membrane / PDZ domain binding / protein kinase C binding / postsynaptic density membrane / Schaffer collateral - CA1 synapse / positive regulation of insulin secretion / nuclear matrix / cell-cell junction / protein transport / presynapse / presynaptic membrane / basolateral plasma membrane / vesicle / non-specific serine/threonine protein kinase / calmodulin binding / protein domain specific binding / phosphorylation / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / neuronal cell body / synapse / dendrite / protein-containing complex binding / nucleolus / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein lin-7 / L27 domain / CASK, SH3 domain / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site ...Protein lin-7 / L27 domain / CASK, SH3 domain / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Helix Hairpins / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peripheral plasma membrane protein CASK / Protein lin-7 homolog B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsFeng, W. / Long, J.-F. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: A unified assembly mode revealed by the structures of tetrameric L27 domain complexes formed by mLin-2/mLin-7 and Patj/Pals1 scaffold proteins.
Authors: Feng, W. / Long, J.F. / Zhang, M.
History
DepositionDec 8, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: lin 7 homolog b
B: Peripheral plasma membrane protein CASK
C: lin 7 homolog b
D: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)24,8824
Polymers24,8824
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 #11minimized average structure

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Components

#1: Protein lin 7 homolog b / mLin-7/Velis/Mals


Mass: 6652.594 Da / Num. of mol.: 2 / Fragment: L27 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: O88951
#2: Protein/peptide Peripheral plasma membrane protein CASK / mLin-2/CASK


Mass: 5788.521 Da / Num. of mol.: 2 / Fragment: L27C domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET32a / Production host: Escherichia coli (E. coli)
References: UniProt: O70589, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
133HNCO, HNCA, HN(CO)CA, HN(CA)CB, CBCA(CO)NH
1443D 13C-separated NOESY
15513C-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM unlabelled L27M/L27C complex in 99.9% D2O; 100mM potassium phosphate99.9% D2O
21.5mM uniformly 15N labelled L27M/L27C complex in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
31.5mM uniformly 15N/13C labelled L27M/L27C complex in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
41.5mM uniformly 15N/13C labelled L27M/L27C complex in 99.9% D2O; 100mM potassium phosphate99.9% D2O
51.5mM 10% 13C labelled L27M/L27C complex in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
Sample conditionsIonic strength: 100mM potassium phosphate / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionClassification
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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