[English] 日本語
Yorodumi- PDB-7nzf: Crystal structure of HLA-DR4 in complex with a mutated human coll... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nzf | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of HLA-DR4 in complex with a mutated human collagen type II peptide | ||||||||||||
Components |
| ||||||||||||
Keywords | IMMUNE SYSTEM / Complex / MHCII | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Ge, C. / Dobritzsch, D. / Holmdahl, R. | ||||||||||||
Funding support | Sweden, 3items
| ||||||||||||
Citation | Journal: Ann Rheum Dis / Year: 2022 Title: Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor. Authors: Ge, C. / Weisse, S. / Xu, B. / Dobritzsch, D. / Viljanen, J. / Kihlberg, J. / Do, N.N. / Schneider, N. / Lanig, H. / Holmdahl, R. / Burkhardt, H. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7nzf.cif.gz | 284.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nzf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nzf_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7nzf_full_validation.pdf.gz | 472.1 KB | Display | |
Data in XML | 7nzf_validation.xml.gz | 18 KB | Display | |
Data in CIF | 7nzf_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/7nzf ftp://data.pdbj.org/pub/pdb/validation_reports/nz/7nzf | HTTPS FTP |
-Related structure data
Related structure data | 7nzeC 7nzhC 7o00C 1j8hS S: Starting model for refinement C: citing same article (ref.) |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20893.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 22432.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||||
#3: Protein/peptide | Mass: 1187.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#4: Sugar | #5: 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: 2.37 Å3/Da / Density % sol: 48.08 % |
---|---|
Crystal grow | Temperature: 290 K / Method: evaporation / Details: 0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91842 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91842 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.9→46.07 Å / Num. obs: 32456 / % possible obs: 99 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.039 / Rrim(I) all: 0.095 / Net I/σ(I): 17.5 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J8H Resolution: 1.9→36.951 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.895 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.167 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.725 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→36.951 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|