+Open data
-Basic information
Entry | Database: PDB / ID: 6d48 | ||||||
---|---|---|---|---|---|---|---|
Title | Cell Surface Receptor | ||||||
Components | Myeloid cell surface antigen CD33 | ||||||
Keywords | IMMUNE SYSTEM / Sialic Acid Binding / Transmembrane / Receptor / Siglec | ||||||
Function / homology | Function and homology information immune response-inhibiting signal transduction / positive regulation of protein tyrosine phosphatase activity / negative regulation of monocyte activation / sialic acid binding / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of calcium ion transport / negative regulation of tumor necrosis factor production / specific granule membrane ...immune response-inhibiting signal transduction / positive regulation of protein tyrosine phosphatase activity / negative regulation of monocyte activation / sialic acid binding / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of calcium ion transport / negative regulation of tumor necrosis factor production / specific granule membrane / positive regulation of protein secretion / cell-cell adhesion / peroxisome / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell signaling / signaling receptor activity / carbohydrate binding / protein phosphatase binding / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / Neutrophil degranulation / Golgi apparatus / cell surface / signal transduction / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.776 Å | ||||||
Authors | Hermans, S.J. / Miles, L.A. / Parker, M.W. | ||||||
Citation | Journal: Iscience / Year: 2019 Title: Small Molecule Binding to Alzheimer Risk Factor CD33 Promotes A beta Phagocytosis. Authors: Miles, L.A. / Hermans, S.J. / Crespi, G.A.N. / Gooi, J.H. / Doughty, L. / Nero, T.L. / Markulic, J. / Ebneth, A. / Wroblowski, B. / Oehlrich, D. / Trabanco, A.A. / Rives, M.L. / Royaux, I. / ...Authors: Miles, L.A. / Hermans, S.J. / Crespi, G.A.N. / Gooi, J.H. / Doughty, L. / Nero, T.L. / Markulic, J. / Ebneth, A. / Wroblowski, B. / Oehlrich, D. / Trabanco, A.A. / Rives, M.L. / Royaux, I. / Hancock, N.C. / Parker, M.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6d48.cif.gz | 204.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6d48.ent.gz | 166.1 KB | Display | PDB format |
PDBx/mmJSON format | 6d48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6d48_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6d48_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 6d48_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 6d48_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/6d48 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/6d48 | HTTPS FTP |
-Related structure data
Related structure data | 6d49C 6d4aC 1nkoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14648.298 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD33, SIGLEC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P20138 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.31 % / Description: Cubic |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 4000 100 mM Tris-HCl pH 8.5 10% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.776→42.48 Å / Num. obs: 51251 / % possible obs: 98.5 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.028 / Rrim(I) all: 0.052 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.776→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2673 / Rpim(I) all: 0.246 / Rrim(I) all: 0.464 / % possible all: 90.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NKO Resolution: 1.776→35.599 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.54 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.776→35.599 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|