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Yorodumi- PDB-6nid: Crystal structure of a human calcium/calmodulin dependent serine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nid | ||||||
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Title | Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide | ||||||
Components |
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Keywords | protein binding/peptide / PDZ domain / MAGUK protein family / peripheral plasma membrane protein / protein binding / c-terminal peptide binding / Neurexin / protein binding-peptide complex | ||||||
Function / homology | Function and homology information gephyrin clustering involved in postsynaptic density assembly / negative regulation of cellular response to growth factor stimulus / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / vocal learning / guanylate kinase activity / neuroligin family protein binding / positive regulation of synapse maturation / neuron cell-cell adhesion ...gephyrin clustering involved in postsynaptic density assembly / negative regulation of cellular response to growth factor stimulus / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / vocal learning / guanylate kinase activity / neuroligin family protein binding / positive regulation of synapse maturation / neuron cell-cell adhesion / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / vocalization behavior / neurotransmitter secretion / acetylcholine receptor binding / Assembly and cell surface presentation of NMDA receptors / calcium ion import / Neurexins and neuroligins / positive regulation of synapse assembly / Nephrin family interactions / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / ciliary membrane / regulation of synaptic vesicle exocytosis / Syndecan interactions / negative regulation of cell-matrix adhesion / adult behavior / positive regulation of calcium ion import / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / Non-integrin membrane-ECM interactions / basement membrane / calcium channel regulator activity / negative regulation of keratinocyte proliferation / positive regulation of synaptic transmission, glutamatergic / cell adhesion molecule binding / synapse assembly / learning / axon guidance / establishment of localization in cell / cell projection / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / protein localization / actin cytoskeleton / signaling receptor activity / presynaptic membrane / basolateral plasma membrane / nuclear membrane / chemical synaptic transmission / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / signaling receptor binding / neuronal cell body / calcium ion binding / nucleolus / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Sun, Y.J. / Gakhar, L. / Fuentes, E.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: CASK PDZ domain specificity Authors: Sun, Y.J. / Hou, T. / Fuentes, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nid.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nid.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 6nid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nid_validation.pdf.gz | 465.5 KB | Display | wwPDB validaton report |
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Full document | 6nid_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 6nid_validation.xml.gz | 14 KB | Display | |
Data in CIF | 6nid_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/6nid ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6nid | HTTPS FTP |
-Related structure data
Related structure data | 6nh9SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 10118.886 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: M 485 Expression artifact G 486 Expression artifact Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Production host: Escherichia coli (E. coli) References: UniProt: O14936, non-specific serine/threonine protein kinase #2: Protein/peptide | Mass: 1318.517 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9ULB1 #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.01M tri-sodium citrate 33% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0003 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: May 12, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0003 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→51.18 Å / Num. obs: 21400 / % possible obs: 96.1 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.056 / Rrim(I) all: 0.081 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2 / Num. unique obs: 2574 / CC1/2: 0.798 / Rpim(I) all: 0.361 / Rrim(I) all: 0.519 / % possible all: 80.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NH9 Resolution: 1.86→41.666 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→41.666 Å
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Refine LS restraints |
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LS refinement shell |
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