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- PDB-7nze: Crystal structure of HLA-DR4 in complex with a human collagen typ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nze | ||||||||||||
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Title | Crystal structure of HLA-DR4 in complex with a human collagen type II peptide | ||||||||||||
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![]() | IMMUNE SYSTEM / Complex / MHCII | ||||||||||||
Function / homology | ![]() collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / Extracellular matrix organization / notochord development ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / Extracellular matrix organization / notochord development / limb bud formation / extracellular matrix structural constituent conferring tensile strength / cartilage development involved in endochondral bone morphogenesis / Collagen biosynthesis and modifying enzymes / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / tissue homeostasis / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / cellular response to BMP stimulus / Signaling by PDGF / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / endochondral ossification / positive regulation of memory T cell differentiation / NCAM1 interactions / collagen fibril organization / cartilage development / proteoglycan binding / transport vesicle membrane / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / polysaccharide binding / cartilage condensation / inner ear morphogenesis / roof of mouth development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Collagen degradation / Generation of second messenger molecules / immunological synapse / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / PD-1 signaling / Integrin cell surface interactions / chondrocyte differentiation / T cell receptor binding / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / MHC class II antigen presentation / visual perception / trans-Golgi network membrane / skeletal system development / central nervous system development / lumenal side of endoplasmic reticulum membrane / sensory perception of sound / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / early endosome membrane / regulation of gene expression / collagen-containing extracellular matrix / adaptive immune response / membrane => GO:0016020 / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ge, C. / Dobritzsch, D. / Holmdahl, R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 587 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.6 KB | Display | ![]() |
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Full document | ![]() | 514 KB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nzfC ![]() 7nzhC ![]() 7o00C ![]() 6bilS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-HLA class II histocompatibility ... , 2 types, 4 molecules AAACCCBBBDDD
#1: Protein | Mass: 21157.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 22432.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein/peptide / Sugars , 2 types, 5 molecules EEEFFF![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Protein/peptide | Mass: 1473.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Sugar | |
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-Non-polymers , 2 types, 350 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.94 % |
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Crystal grow | Temperature: 290 K / Method: evaporation Details: 20% polyethylene glycol 3350 and 200 mM ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.05→47.009 Å / Num. obs: 62583 / % possible obs: 98.1 % / Redundancy: 1 % / CC1/2: 0.999 / Net I/σ(I): 8.2 | |||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6BIL Resolution: 2.05→47.009 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.368 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.184 / ESU R Free: 0.174 Details: Hydrogens have been added in their riding positions
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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: 46.285 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→47.009 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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