[English] 日本語
Yorodumi- PDB-3wex: Crystal structure of HLA-DP5 in complex with Cry j 1-derived pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wex | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of HLA-DP5 in complex with Cry j 1-derived peptide (residues 214-222) | ||||||
Components | (MHC class II antigen) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin Fold / Antigen Presentation / T Cell Receptor / Cell Surface | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / membrane => GO:0016020 / endosome membrane / lysosomal membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kusano, S. / Kukimoto-Niino, M. / Shirouzu, M. / Yokoyama, S. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2014 Title: Structural basis for the specific recognition of the major antigenic peptide from the Japanese cedar pollen allergen Cry j 1 by HLA-DP5 Authors: Kusano, S. / Kukimoto-Niino, M. / Satta, Y. / Ohsawa, N. / Uchikubo-Kamo, T. / Wakiyama, M. / Ikeda, M. / Terada, T. / Yamamoto, K. / Nishimura, Y. / Shirouzu, M. / Sasazuki, T. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wex.cif.gz | 320.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wex.ent.gz | 261.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/3wex ftp://data.pdbj.org/pub/pdb/validation_reports/we/3wex | HTTPS FTP |
---|
-Related structure data
Related structure data | 3lqzS 3wey S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22230.660 Da / Num. of mol.: 4 / Fragment: extracellular domain, UNP residues 32-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: baculovirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I2G9G1 #2: Protein | Mass: 25254.139 Da / Num. of mol.: 4 / Fragment: extracellular domain, UNP residues 1-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: baculovirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I2FL84 #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 24% (w/v) PEG 3350, 0.2M Ammonium nitrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2011 | ||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→64.28 Å / Num. obs: 70445 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.06 Å2 / Rsym value: 0.201 / Net I/σ(I): 12.31 | ||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LQZ Resolution: 2.4→64.279 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8152 / SU ML: 0.28 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.93 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.32 Å2 / Biso mean: 29.2 Å2 / Biso min: 8.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→64.279 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
|