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Yorodumi- PDB-1zl8: NMR structure of L27 heterodimer from C. elegans Lin-7 and H. sap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zl8 | ||||||
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Title | NMR structure of L27 heterodimer from C. elegans Lin-7 and H. sapiens Lin-2 scaffold proteins | ||||||
Components |
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Keywords | PROTEIN BINDING / heterodimer / L27 / alpha helix / scaffold / assembly / specificity / signaling | ||||||
Function / homology | Function and homology information negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins ...negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / ciliary membrane / regulation of synaptic vesicle exocytosis / Syndecan interactions / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / basement membrane / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / phosphorylation / 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 | ||||||
Biological species | Caenorhabditis elegans (invertebrata) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing | ||||||
Authors | Petrosky, K.Y. / Ou, H.D. / Lohr, F. / Dotsch, V. / Lim, W.A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zl8.cif.gz | 339.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zl8.ent.gz | 279.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/1zl8 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/1zl8 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details | Contents: 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 |
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Sample conditions | Ionic strength: 0 / pH: 8.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry simulated annealing / Software ordinal: 1 Details: The structures are based on 1544 NOE-derived distance constraints and 204 dihedral angle restraints. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |