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- PDB-1zl8: NMR structure of L27 heterodimer from C. elegans Lin-7 and H. sap... -

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Basic information

Entry
Database: PDB / ID: 1zl8
TitleNMR structure of L27 heterodimer from C. elegans Lin-7 and H. sapiens Lin-2 scaffold proteins
Components
  • LIN-7
  • Peripheral plasma membrane protein CASK
KeywordsPROTEIN BINDING / heterodimer / L27 / alpha helix / scaffold / assembly / specificity / signaling
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / GMP kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / calcium ion import / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors ...negative regulation of cellular response to growth factor stimulus / GMP kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / calcium ion import / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors / Sensory processing of sound by outer hair cells of the cochlea / Neurexins and neuroligins / Sensory processing of sound by inner hair cells of the cochlea / ciliary membrane / Syndecan interactions / regulation of synaptic vesicle exocytosis / positive regulation of calcium ion import / basement membrane / negative regulation of cell-matrix adhesion / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell junction / intracellular protein localization / cell-cell junction / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / cell adhesion / signaling receptor binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / LIN-7
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Homo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsPetrosky, K.Y. / Ou, H.D. / Lohr, F. / Dotsch, V. / Lim, W.A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A General Model for Preferential Hetero-oligomerization of LIN-2/7 Domains: Mechanism Underlying Directed Assembly of Supramolecular Signaling Complexes
Authors: Petrosky, K.Y. / Ou, H.D. / Lohr, F. / Dotsch, V. / Lim, W.A.
History
DepositionMay 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIN-7
B: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)12,2782
Polymers12,2782
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein LIN-7


Mass: 6086.837 Da / Num. of mol.: 1 / Fragment: L27 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: LIN7 / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 1685067, UniProt: P90976*PLUS
#2: Protein Peripheral plasma membrane protein CASK / hCASK / Calcium/calmodulin-dependent serine protein kinase / Lin-2 homolog


Mass: 6190.877 Da / Num. of mol.: 1 / Fragment: L27 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O14936, 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
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 2mM Lin-7/Lin-2C; 20mM HEPES, 5mM TCEP, 0.05% DSS, 0.05% sodium azide, 90% H2O, 10% D2O
Solvent system: 90% D2O, 10% D2O
Sample conditionsIonic strength: 0 / pH: 8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX9001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR4.5Brukercollection
XEASY1.3Bartels, Xia, Billeter, Guntert, Wuthrichdata analysis
DYANA1.5Guntert, Mumenthaler, Wuthrichstructure solution
CNS1.1Brungerrefinement
TALOS98.040.21.02Cornilescu and Baxprocessing
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on 1544 NOE-derived distance constraints and 204 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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