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Open data
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Basic information
Entry | Database: PDB / ID: 6b8o | ||||||
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Title | WT Ig-like V Domain with Phosphatidylserine | ||||||
![]() | Triggering receptor expressed on myeloid cells 2 | ||||||
![]() | SIGNALING PROTEIN / Membrane receptor | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sudom, A. / Wang, Z. | ||||||
![]() | ![]() Title: Molecular basis for the loss-of-function effects of the Alzheimer's disease-associated R47H variant of the immune receptor TREM2. Authors: Sudom, A. / Talreja, S. / Danao, J. / Bragg, E. / Kegel, R. / Min, X. / Richardson, J. / Zhang, Z. / Sharkov, N. / Marcora, E. / Thibault, S. / Bradley, J. / Wood, S. / Lim, A.C. / Chen, H. ...Authors: Sudom, A. / Talreja, S. / Danao, J. / Bragg, E. / Kegel, R. / Min, X. / Richardson, J. / Zhang, Z. / Sharkov, N. / Marcora, E. / Thibault, S. / Bradley, J. / Wood, S. / Lim, A.C. / Chen, H. / Wang, S. / Foltz, I.N. / Sambashivan, S. / Wang, Z. #1: ![]() Title: Structure of Ig-like V domain in complex with phosphatidylserine to 2.2 Angstrom resolution Authors: Sudom, A. / Wang, Z. / Min, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.9 KB | Display | ![]() |
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PDB format | ![]() | 117.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ud7SC ![]() 5ud8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 12 molecules ABCDEF![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 19138.254 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 113 molecules ![](data/chem/img/IOD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PSF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PSF.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IOD / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.2 M NaI, 1.6 M ammonium sulfate, 50 mM Tris 8.5 |
-Data collection
Diffraction | Mean temperature: 80 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.2→47.36 Å / Num. obs: 57469 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Net I/σ(I): 19.8 / Num. measured all: 752391 / Scaling rejects: 0 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UD7 Resolution: 2.2→47.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.77 / SU ML: 0.142 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.184 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.23 Å2 / Biso mean: 52.028 Å2 / Biso min: 19.21 Å2
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Refinement step | Cycle: final / Resolution: 2.2→47.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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