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Yorodumi- PDB-4arn: Crystal structure of the N-terminal domain of Drosophila Toll receptor -
+Open data
-Basic information
Entry | Database: PDB / ID: 4arn | |||||||||
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Title | Crystal structure of the N-terminal domain of Drosophila Toll receptor | |||||||||
Components | TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA | |||||||||
Keywords | IMMUNE SYSTEM / CYTOKINE RECEPTOR / EMBRYONIC DEVELOPMENT / INNATE IMMUNITY / LEUCINE-RICH REPEAT / LRR HYBRID TECHNOLOGY | |||||||||
Function / homology | Function and homology information positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / defense response to oomycetes / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / synaptic target inhibition / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' ...positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / defense response to oomycetes / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / synaptic target inhibition / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' / positive regulation of antifungal peptide production / TIR domain binding / cell competition in a multicellular organism / larval somatic muscle development / positive regulation of antimicrobial peptide production / antifungal innate immune response / Neutrophil degranulation / dorsal/ventral axis specification / Toll signaling pathway / detection of virus / NAD+ nucleotidase, cyclic ADP-ribose generating / virion binding / cytokine receptor activity / negative regulation of multicellular organism growth / cytokine binding / cleavage furrow / negative regulation of insulin receptor signaling pathway / synapse assembly / negative regulation of cell growth / transmembrane signaling receptor activity / response to wounding / signaling receptor activity / heart development / early endosome / cell adhesion / defense response to Gram-positive bacterium / external side of plasma membrane / innate immune response / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) EPTATRETUS BURGERI (inshore hagfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | |||||||||
Authors | Gangloff, M. / Gay, N.J. | |||||||||
Citation | Journal: Structure / Year: 2013 Title: Functional Insights from the Crystal Structure of the N-Terminal Domain of the Prototypical Toll Receptor. Authors: Gangloff, M. / Arnot, C.J. / Lewis, M. / Gay, N.J. #1: Journal: J.Appl.Crystallogr. / Year: 2013 Title: Liesegang-Like Patterns of Toll Crystals Grown in Gel. Authors: Gangloff, M. / Moreno, A. / Gay, N.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4arn.cif.gz | 463 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4arn.ent.gz | 385 KB | Display | PDB format |
PDBx/mmJSON format | 4arn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4arn_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4arn_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4arn_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 4arn_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/4arn ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4arn | HTTPS FTP |
-Related structure data
Related structure data | 4arrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 31957.838 Da / Num. of mol.: 4 Fragment: TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201 Source method: isolated from a genetically manipulated source Details: CHIMERIC PROTEIN Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly), (gene. exp.) EPTATRETUS BURGERI (inshore hagfish) Plasmid: PFASTBAC-1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P08953, UniProt: Q4G1L2 |
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-Sugars , 4 types, 9 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 325 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | VARIABLE LYMPHOCYTE |
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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: 3.29 Å3/Da / Density % sol: 62.59 % / Description: NONE |
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Crystal grow | pH: 7 / Details: PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.9 Å / Num. obs: 72977 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 61.38 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.41→2.54 Å / Redundancy: 6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.1 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ARR Resolution: 2.41→29.95 Å / Cor.coef. Fo:Fc: 0.9335 / Cor.coef. Fo:Fc free: 0.9281 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.185 Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM
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Displacement parameters | Biso mean: 66.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.395 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→29.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.47 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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