+Open data
-Basic information
Entry | Database: PDB / ID: 4ofy | |||||||||
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Title | Crystal Structure of the Complex of SYG-1 D1-D2 and SYG-2 D1-D4 | |||||||||
Components |
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Keywords | CELL ADHESION / Immunoglobulin superfamily / Synaptogenesis / Protein Binding / N-linked Glycosylation / Membrane / Extracellular / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information Nephrin family interactions / protein complex involved in cell adhesion / synaptic target recognition / branching morphogenesis of a nerve / collateral sprouting / protein localization to synapse / actin filament bundle assembly / cell adhesion molecule binding / synapse assembly / synaptic membrane ...Nephrin family interactions / protein complex involved in cell adhesion / synaptic target recognition / branching morphogenesis of a nerve / collateral sprouting / protein localization to synapse / actin filament bundle assembly / cell adhesion molecule binding / synapse assembly / synaptic membrane / cell-cell adhesion / synapse organization / cell-cell junction / cell-cell signaling / axon / synapse / protein-containing complex binding / protein homodimerization activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Ozkan, E. / Garcia, K.C. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2014 Title: Extracellular Architecture of the SYG-1/SYG-2 Adhesion Complex Instructs Synaptogenesis. Authors: Ozkan, E. / Chia, P.H. / Wang, R.R. / Goriatcheva, N. / Borek, D. / Otwinowski, Z. / Walz, T. / Shen, K. / Garcia, K.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ofy.cif.gz | 382.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ofy.ent.gz | 309.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ofy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/4ofy ftp://data.pdbj.org/pub/pdb/validation_reports/of/4ofy | HTTPS FTP |
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-Related structure data
Related structure data | 4of0C 4of3SC 4of6C 4of7C 4of8C 4ofdC 4ofiC 4ofkC 4ofpSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 29085.717 Da / Num. of mol.: 3 / Fragment: D1-D2, UNP residues 19-271 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_K02E10.8, K02E10.8, syg-1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: B1Q236 #2: Protein | Mass: 46913.484 Da / Num. of mol.: 3 / Fragment: D1-D4, UNP residues 20-430 / Mutation: N391C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C26G2.1, CELE_C26G2.1, syg-2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q9U3P2 #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Chemical | |
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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: 3.41 Å3/Da / Density % sol: 63.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 16% PEG 3,350, 0.2 M Triammonium citrate, 0.1 M MES pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0088 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2008 |
Radiation | Monochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0088 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 44725 / Num. obs: 44580 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 90.89 Å2 / Rsym value: 0.098 / Net I/σ(I): 13.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entries 4OF3, 4OFP Resolution: 3.3→41.061 Å / SU ML: 0.5 / σ(F): 0 / Phase error: 39.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→41.061 Å
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Refine LS restraints |
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LS refinement shell |
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