+Open data
-Basic information
Entry | Database: PDB / ID: 6nix | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Immune Receptor | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / HLA / MHC / Rheumatoid Arthritis | ||||||
Function / homology | Function and homology information 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 structural constituent conferring tensile strength / regulation of interleukin-4 production ...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 structural constituent conferring tensile strength / regulation of interleukin-4 production / Extracellular matrix organization / notochord development / limb bud formation / regulation of interleukin-10 production / Collagen biosynthesis and modifying enzymes / cartilage development involved in endochondral bone morphogenesis / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of monocyte differentiation / CD4 receptor binding / NCAM1 interactions / positive regulation of kinase activity / inflammatory response to antigenic stimulus / collagen fibril organization / cartilage development / proteoglycan binding / transport vesicle membrane / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / intermediate filament / inner ear morphogenesis / polysaccharide binding / T-helper 1 type immune response / cartilage condensation / roof of mouth development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / 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 / epidermis development / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / extrinsic apoptotic signaling pathway in absence of ligand / MHC class II antigen presentation / visual perception / trans-Golgi network membrane / central nervous system development / skeletal system development / lumenal side of endoplasmic reticulum membrane / protein tetramerization / sensory perception of sound / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / 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 / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / regulation of gene expression / positive regulation of canonical NF-kappaB signal transduction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ting, Y.T. / Reid, H.H. / Rossjohn, J. | ||||||
Citation | Journal: To Be Published Title: Immune Receptor Authors: Ting, Y.T. / Reid, H.H. / Rossjohn, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6nix.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6nix.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 6nix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/6nix ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6nix | HTTPS FTP |
---|
-Related structure data
Related structure data | 4mcyS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21919.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P01903 |
---|---|
#2: Protein | Mass: 23224.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P13760 |
-Protein/peptide / Sugars , 2 types, 4 molecules C
#3: Protein/peptide | Mass: 1473.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02458*PLUS |
---|---|
#4: Sugar |
-Non-polymers , 2 types, 167 molecules
#5: Chemical | ChemComp-B3P / |
---|---|
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.24 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 20-30% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→89.02 Å / Num. obs: 26942 / % possible obs: 98.4 % / Redundancy: 5.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.043 / Rrim(I) all: 0.107 / Net I/σ(I): 9.6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MCY Resolution: 2.1→89.02 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.304 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.182 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.46 Å2 / Biso mean: 46.023 Å2 / Biso min: 22.89 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→89.02 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|