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Yorodumi- PDB-6yye: TREM2 extracellular domain (19-131) in complex with single-chain ... -
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-Basic information
Entry | Database: PDB / ID: 6yye | ||||||
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Title | TREM2 extracellular domain (19-131) in complex with single-chain variable fragment (scFv-2) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / scFv / complex / receptor / Alzheimer's | ||||||
Function / homology | Function and homology information positive regulation of high-density lipoprotein particle clearance / regulation of toll-like receptor 6 signaling pathway / positive regulation of complement activation, classical pathway / detection of lipoteichoic acid / regulation of macrophage inflammatory protein 1 alpha production / regulation of hippocampal neuron apoptotic process / regulation of plasma membrane bounded cell projection organization / positive regulation of inward rectifier potassium channel activity / positive regulation of C-C chemokine receptor CCR7 signaling pathway / positive regulation of CAMKK-AMPK signaling cascade ...positive regulation of high-density lipoprotein particle clearance / regulation of toll-like receptor 6 signaling pathway / positive regulation of complement activation, classical pathway / detection of lipoteichoic acid / regulation of macrophage inflammatory protein 1 alpha production / regulation of hippocampal neuron apoptotic process / regulation of plasma membrane bounded cell projection organization / positive regulation of inward rectifier potassium channel activity / positive regulation of C-C chemokine receptor CCR7 signaling pathway / positive regulation of CAMKK-AMPK signaling cascade / excitatory synapse pruning / positive regulation of CD40 signaling pathway / negative regulation of cell activation / detection of peptidoglycan / positive regulation of macrophage fusion / import into cell / negative regulation of macrophage colony-stimulating factor signaling pathway / sulfatide binding / positive regulation of engulfment of apoptotic cell / regulation of intracellular signal transduction / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / negative regulation of fat cell proliferation / lipoteichoic acid binding / positive regulation of establishment of protein localization / positive regulation of synapse pruning / microglial cell activation involved in immune response / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of astrocyte activation / apolipoprotein A-I binding / respiratory burst after phagocytosis / positive regulation of low-density lipoprotein particle clearance / positive regulation of microglial cell migration / negative regulation of autophagic cell death / detection of lipopolysaccharide / Other semaphorin interactions / CXCL12-activated CXCR4 signaling pathway / very-low-density lipoprotein particle binding / negative regulation of sequestering of triglyceride / negative regulation of p38MAPK cascade / high-density lipoprotein particle binding / negative regulation of neuroinflammatory response / negative regulation of glial cell apoptotic process / negative regulation of toll-like receptor 4 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / regulation of resting membrane potential / negative regulation of NLRP3 inflammasome complex assembly / microglial cell proliferation / dendritic cell differentiation / complement-mediated synapse pruning / positive regulation of microglial cell activation / regulation of TOR signaling / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of phagocytosis, engulfment / positive regulation of chemotaxis / cellular response to peptidoglycan / phagocytosis, recognition / peptidoglycan binding / positive regulation of proteasomal protein catabolic process / negative regulation of cholesterol storage / positive regulation of amyloid-beta clearance / phosphatidylethanolamine binding / kinase activator activity / lipid homeostasis / positive regulation of osteoclast differentiation / negative regulation of amyloid fibril formation / positive regulation of kinase activity / cellular response to lipid / apoptotic cell clearance / regulation of interleukin-6 production / negative regulation of interleukin-1 beta production / dendritic spine maintenance / positive regulation of cholesterol efflux / positive regulation of ATP biosynthetic process / phagocytosis, engulfment / regulation of innate immune response / phosphatidylserine binding / pyroptotic inflammatory response / regulation of cytokine production involved in inflammatory response / plasma membrane raft / lipoprotein particle binding / regulation of peptidyl-tyrosine phosphorylation / cellular response to lipoteichoic acid / apolipoprotein binding / positive regulation of interleukin-10 production / social behavior / humoral immune response / negative regulation of tumor necrosis factor production / regulation of lipid metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to axon injury / negative regulation of cytokine production involved in inflammatory response / positive regulation of TOR signaling / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / negative regulation of inflammatory response to antigenic stimulus / positive regulation of calcium-mediated signaling / astrocyte activation / positive regulation of protein localization to plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å | ||||||
Authors | Szykowska, A. / Preger, C. / Krojer, T. / Mukhopadhyay, S.M.M. / McKinley, G. / Graslund, S. / Wigren, E. / Persson, H. / von Delft, F. / Arrowsmith, C.H. ...Szykowska, A. / Preger, C. / Krojer, T. / Mukhopadhyay, S.M.M. / McKinley, G. / Graslund, S. / Wigren, E. / Persson, H. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Di Daniel, E. / Burgess-Brown, N. / Bullock, A. | ||||||
Citation | Journal: Structure / Year: 2021 Title: Selection and structural characterization of anti-TREM2 scFvs that reduce levels of shed ectodomain. Authors: Szykowska, A. / Chen, Y. / Smith, T.B. / Preger, C. / Yang, J. / Qian, D. / Mukhopadhyay, S.M. / Wigren, E. / Neame, S.J. / Graslund, S. / Persson, H. / Atkinson, P.J. / Di Daniel, E. / ...Authors: Szykowska, A. / Chen, Y. / Smith, T.B. / Preger, C. / Yang, J. / Qian, D. / Mukhopadhyay, S.M. / Wigren, E. / Neame, S.J. / Graslund, S. / Persson, H. / Atkinson, P.J. / Di Daniel, E. / Mead, E. / Wang, J. / Davis, J.B. / Burgess-Brown, N.A. / Bullock, A.N. #1: Journal: Biorxiv / Year: 2021 Title: Selection and structural characterisation of anti-TREM2 scFvs that reduce levels of shed ectodomain Authors: Szykowska, A. / Chen, Y. / Smith, T.B. / Preger, C. / Yang, J. / Qian, D. / Mukhopadhyay, S. / Wigren, E. / Neame, S.J. / Graslund, S. / Persson, H. / Atkinson, P.J. / Di Daniel, E. / Mead, ...Authors: Szykowska, A. / Chen, Y. / Smith, T.B. / Preger, C. / Yang, J. / Qian, D. / Mukhopadhyay, S. / Wigren, E. / Neame, S.J. / Graslund, S. / Persson, H. / Atkinson, P.J. / Di Daniel, E. / Mead, E. / Wang, J. / Davis, J.B. / Burgess-Brown, N.A. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yye.cif.gz | 317.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yye.ent.gz | 220.5 KB | Display | PDB format |
PDBx/mmJSON format | 6yye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yye_validation.pdf.gz | 471.3 KB | Display | wwPDB validaton report |
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Full document | 6yye_full_validation.pdf.gz | 477.5 KB | Display | |
Data in XML | 6yye_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 6yye_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/6yye ftp://data.pdbj.org/pub/pdb/validation_reports/yy/6yye | HTTPS FTP |
-Related structure data
Related structure data | 6y6cC 6ymqC 6cy6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12951.615 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MHNTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLAD Source: (gene. exp.) Homo sapiens (human) / Gene: TREM2 / Production host: Homo sapiens (human) / References: UniProt: Q9NZC2 #2: Antibody | Mass: 26200.885 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) #3: Sugar | ChemComp-NAG / | Has ligand of interest | N | |
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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: 5.39 Å3/Da / Density % sol: 77.18 % / Description: Large cubes |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.015M nickel chloride,0.1M tris pH 8.5,2.2M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9763 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.356→110.07 Å / Num. obs: 16278 / % possible obs: 92 % / Redundancy: 13.4 % / Biso Wilson estimate: 79.88 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.356→3.679 Å / Num. unique obs: 814 / CC1/2: 0.749 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CY6 Resolution: 3.36→110.07 Å / SU ML: 0.5925 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.8277 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.36→110.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -26.1951235583 Å / Origin y: -30.813459225 Å / Origin z: -57.1322426139 Å
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Refinement TLS group | Selection details: all |