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Yorodumi- PDB-6eg0: Crystal structure of Dpr4 Ig1-Ig2 in complex with DIP-Eta Ig1-Ig3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eg0 | |||||||||
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Title | Crystal structure of Dpr4 Ig1-Ig2 in complex with DIP-Eta Ig1-Ig3 | |||||||||
Components |
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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 / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / A tetrasaccharide linker sequence is required for GAG synthesis / neuron projection membrane / sensory perception of chemical stimulus / synapse organization ...Degradation of the extracellular matrix / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / A tetrasaccharide linker sequence is required for GAG synthesis / neuron projection membrane / sensory perception of chemical stimulus / 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 | 6eg0.cif.gz | 128.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eg0.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 6eg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eg0_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6eg0_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6eg0_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 6eg0_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/6eg0 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/6eg0 | HTTPS FTP |
-Related structure data
Related structure data | 6efyC 6efzC 6eg1C 4cmmS 5eo9S 5k6uS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 24741.758 Da / Num. of mol.: 1 / Fragment: UNP residues 32-246 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: dpr4, CG12593, CG14707, CT34497, Dmel\CG33512, Dpr-4, Dpr4, dpr4-RA, CG33512, Dmel_CG33512 Production host: Homo sapiens (human) / References: UniProt: Q59DX6 |
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#2: Protein | Mass: 34982.965 Da / Num. of mol.: 1 / Fragment: UNP residues 31-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: DIP-eta, 14010, CT33567, Dmel\CG14010, CG14010, Dmel_CG14010 Production host: Homo sapiens (human) / References: UniProt: Q9VMN9 |
-Sugars , 5 types, 5 molecules
#3: 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 |
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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-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 |
#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-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 |
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-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 |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 52 molecules
#8: Chemical | #9: Chemical | ChemComp-EDO / | #10: Chemical | #11: 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: 4.76 Å3/Da / Density % sol: 74.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 28% Edo_p8k (Molecular Dimensions), 0.1 M Morpheus Buffer 2, pH 7.5 (Molecular Dimensions), 10% carboxylic acid (Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2016 |
Radiation | Monochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→106.2 Å / Num. obs: 24914 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 62.780981968 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Rmerge(I) obs: 0.686 / Num. unique obs: 3936 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 5EO9, 4CMM, & 5K6U Resolution: 2.9→19.987 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.987 Å
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Refine LS restraints |
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LS refinement shell |
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