+Open data
-Basic information
Entry | Database: PDB / ID: 8w8t | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human CLEC12A CRD | ||||||
Components | C-type lectin domain family 12 member A | ||||||
Keywords | IMMUNE SYSTEM / Pattern Recognition Receptor / Innate immunitiy / C-type lectin receptor / DAMPs | ||||||
Function / homology | Function and homology information signaling receptor regulator activity / tertiary granule membrane / specific granule membrane / transmembrane signaling receptor activity / carbohydrate binding / Neutrophil degranulation / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Mori, S. / Nagae, M. / Yamasaki, S. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Int.Immunol. / Year: 2024 Title: Crystal structure of the complex of CLEC12A and an antibody that interferes with binding of diverse ligands. Authors: Mori, S. / Nagae, M. / Yamasaki, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8w8t.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8w8t.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 8w8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/8w8t ftp://data.pdbj.org/pub/pdb/validation_reports/w8/8w8t | HTTPS FTP |
---|
-Related structure data
Related structure data | 8w9hC 8w9jC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14738.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC12A / Production host: Homo sapiens (human) / References: UniProt: Q5QGZ9 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.91 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Sodium cacodylate (pH 6.5), 0.2M Ammonium sulfate, 30% polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.53 Å / Num. obs: 13302 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 30.59 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.062 / Rrim(I) all: 0.266 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1252 / CC1/2: 0.74 / Rpim(I) all: 0.343 / Rrim(I) all: 1.545 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.16 Å / SU ML: 0.3346 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4694 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.39 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→42.16 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -8.73189719608 Å / Origin y: 0.789731117558 Å / Origin z: -15.5052739975 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |