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- PDB-3wex: Crystal structure of HLA-DP5 in complex with Cry j 1-derived pept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wex | ||||||
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Title | Crystal structure of HLA-DP5 in complex with Cry j 1-derived peptide (residues 214-222) | ||||||
![]() | (MHC class II antigen) x 2 | ||||||
![]() | IMMUNE SYSTEM / Immunoglobulin Fold / Antigen Presentation / T Cell Receptor / Cell Surface | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kusano, S. / Kukimoto-Niino, M. / Shirouzu, M. / Yokoyama, S. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 320.8 KB | Display | ![]() |
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PDB format | ![]() | 261.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3lqzS ![]() 3wey S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.05 % |
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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 | ||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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 max: 96.32 Å2 / Biso mean: 29.2 Å2 / Biso min: 8.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→64.279 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
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