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Yorodumi- PDB-1jc7: The Laminin-Binding Domain of Agrin is Structurally Related to N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jc7 | ||||||
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Title | The Laminin-Binding Domain of Agrin is Structurally Related to N-TIMP-1 | ||||||
Components | Agrin | ||||||
Keywords | CELL ADHESION / NEUROMUSCULAR JUNCTION / AGRIN / INTERACTION COILED-DOIL PROTEINS WITH GLOBULAR PROTEINS / OB-FOLD / TIMP | ||||||
Function / homology | Function and homology information extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / dystroglycan binding / basal part of cell ...extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / dystroglycan binding / basal part of cell / photoreceptor ribbon synapse / filopodium assembly / glycosaminoglycan binding / extracellular matrix binding / heparan sulfate proteoglycan binding / positive regulation of filopodium assembly / neuromuscular junction development / transmembrane receptor protein tyrosine kinase activator activity / receptor clustering / basement membrane / laminin binding / extracellular matrix / brain development / neuromuscular junction / G protein-coupled acetylcholine receptor signaling pathway / positive regulation of GTPase activity / negative regulation of neuron projection development / signaling receptor activity / heparin binding / nervous system development / actin cytoskeleton organization / cell differentiation / membrane raft / axon / glutamatergic synapse / synapse / calcium ion binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.73 Å | ||||||
Authors | Stetefeld, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: The laminin-binding domain of agrin is structurally related to N-TIMP-1. Authors: Stetefeld, J. / Jenny, M. / Schulthess, T. / Landwehr, R. / Schumacher, B. / Frank, S. / Ruegg, M.A. / Engel, J. / Kammerer, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jc7.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jc7.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/1jc7 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/1jc7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15147.343 Da / Num. of mol.: 1 / Fragment: LAMININ-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: Q90685, UniProt: P31696*PLUS |
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#2: Chemical | ChemComp-CL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.34 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.847 Å |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.847 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 26.4 Å2 |
Reflection | *PLUS Highest resolution: 2.7 Å / % possible obs: 99.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 94.3 % / Rmerge(I) obs: 0.272 |
-Processing
Software |
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Refinement | Resolution: 2.73→27.92 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 664563.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.06 Å2 / ksol: 0.304 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.73→27.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.342 / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.316 |