+Open data
-Basic information
Entry | Database: PDB / ID: 6efy | |||||||||
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Title | Crystal Structure of DIP-Alpha Ig1-3 | |||||||||
Components | Dpr-interacting protein alpha, isoform A | |||||||||
Keywords | CELL ADHESION / Immunoglobulin Super-Family / Synaptic specification / nervous system development / cell-surface protein | |||||||||
Function / homology | Function and homology information Degradation of the extracellular matrix / Integrin cell surface interactions / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / A tetrasaccharide linker sequence is required for GAG synthesis / neuron projection membrane / synapse organization / neuron projection / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Cosmanescu, F. / Shapiro, L. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Neuron / Year: 2018 Title: Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins. Authors: Cosmanescu, F. / Katsamba, P.S. / Sergeeva, A.P. / Ahlsen, G. / Patel, S.D. / Brewer, J.J. / Tan, L. / Xu, S. / Xiao, Q. / Nagarkar-Jaiswal, S. / Nern, A. / Bellen, H.J. / Zipursky, S.L. / ...Authors: Cosmanescu, F. / Katsamba, P.S. / Sergeeva, A.P. / Ahlsen, G. / Patel, S.D. / Brewer, J.J. / Tan, L. / Xu, S. / Xiao, Q. / Nagarkar-Jaiswal, S. / Nern, A. / Bellen, H.J. / Zipursky, S.L. / Honig, B. / Shapiro, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6efy.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6efy.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 6efy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/6efy ftp://data.pdbj.org/pub/pdb/validation_reports/ef/6efy | HTTPS FTP |
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-Related structure data
Related structure data | 6efzC 6eg0C 6eg1C 5eo9S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34503.098 Da / Num. of mol.: 1 / Fragment: UNP residues 40-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: DIP-alpha, 32791, CG13019, CG13020, Dmel\CG32791, CG32791, Dmel_CG32791 Production host: Homo sapiens (human) / References: UniProt: Q9W4R3 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.77 Å3/Da / Density % sol: 74.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 2% PEG3350, 17% Tacsimate, pH 7.0, 0.1 M HEPES, pH 7.0, cryoprotectant: 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2016 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→67.78 Å / Num. obs: 14611 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 79.9577746632 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.784 / Num. unique obs: 2349 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EO9 Resolution: 2.9→19.938 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.938 Å
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Refine LS restraints |
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LS refinement shell |
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