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- PDB-1rso: Hetero-tetrameric L27 (Lin-2, Lin-7) domain complexes as organiza... -

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Basic information

Entry
Database: PDB / ID: 1rso
TitleHetero-tetrameric L27 (Lin-2, Lin-7) domain complexes as organization platforms of supra-molecular assemblies
Components
  • Peripheral plasma membrane protein CASK
  • Presynaptic protein SAP97Synapse
KeywordsNEUROPEPTIDE/MEMBRANE PROTEIN / L27 domain / scaffold protein / protein assembly / cell polarity / NEUROPEPTIDE-MEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


podocyte foot / tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / negative regulation of cellular response to growth factor stimulus / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development ...podocyte foot / tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / negative regulation of cellular response to growth factor stimulus / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / Neurexins and neuroligins / establishment of centrosome localization / Dopamine Neurotransmitter Release Cycle / negative regulation of p38MAPK cascade / cortical microtubule organization / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / neurexin family protein binding / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / regulation of neurotransmitter secretion / negative regulation of wound healing / peristalsis / nuclear lamina / positive regulation of dendritic spine morphogenesis / cell projection membrane / paranode region of axon / smooth muscle tissue development / bicellular tight junction assembly / Trafficking of AMPA receptors / positive regulation of potassium ion transport / Activation of Ca-permeable Kainate Receptor / apical dendrite / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / calcium ion import / amyloid precursor protein metabolic process / endothelial cell proliferation / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / ureteric bud development / ciliary membrane / regulation of myelination / cortical actin cytoskeleton organization / regulation of synaptic vesicle exocytosis / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / receptor clustering / positive regulation of calcium ion import / postsynaptic density, intracellular component / microvillus / kinesin binding / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / bicellular tight junction / potassium channel regulator activity / negative regulation of keratinocyte proliferation / phosphatase binding / T cell proliferation / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of T cell proliferation / T-tubule / ionotropic glutamate receptor binding / actin filament polymerization / regulation of membrane potential / T cell activation / basal plasma membrane / protein kinase C binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization / PDZ domain binding / establishment of localization in cell / protein localization to plasma membrane / postsynaptic density membrane / positive regulation of protein localization to plasma membrane / Schaffer collateral - CA1 synapse / neuromuscular junction / protein localization / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / positive regulation of insulin secretion / cell-cell adhesion / synaptic vesicle membrane / cerebral cortex development / nuclear matrix / regulation of protein localization / negative regulation of epithelial cell proliferation
Similarity search - Function
L27 domain / Helix hairpin bin / CASK, SH3 domain / L27-1 / L27_1 / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. ...L27 domain / Helix hairpin bin / CASK, SH3 domain / L27-1 / L27_1 / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / 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 / SH3 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
Disks large homolog 1 / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsFeng, W. / Long, J.-F. / Fan, J.-S. / Suetake, T. / Zhang, M.
CitationJournal: NAT.STRUCT.MOL.BIOL. / Year: 2004
Title: The tetrameric L27 domain complex as an organization platform for supramolecular assemblies
Authors: Feng, W. / Long, J.-F. / Fan, J.-S. / Suetake, T. / Zhang, M.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Presynaptic protein SAP97
B: Peripheral plasma membrane protein CASK
C: Presynaptic protein SAP97
D: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)27,1304
Polymers27,1304
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 Presynaptic protein SAP97 / Synapse / SAP97


Mass: 7236.097 Da / Num. of mol.: 2 / Fragment: L27 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q62696
#2: Protein Peripheral plasma membrane protein CASK / mLin-2/CASK


Mass: 6329.000 Da / Num. of mol.: 2 / Fragment: L27N domain / Mutation: C363S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET / Production host: Escherichia coli (E. coli)
References: UniProt: Q62915, 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 L27S/L27N complex in 99.9% D2O; 100mM potassium phosphate99.9% D2O
21.5mM uniformly 15N labelled L27S/L27N complex in 90% H2O/10% D2O; 100mM potassium phosphate90% H2O/10% D2O
31.5mM uniformly 15N/13C labelled L27S/L27N complex in 90% H2O/10% D2O; 100mM potassium phosphate90% H2O/10% D2O
41.5mM uniformly 15N/13C labelled L27S/L27N complex in 99.9% D2O; 100mM potassium phosphate99.9% D2O
51.5mM 10% 13C labelled L27S/L27N 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
NameVersionDeveloperClassification
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
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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