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Yorodumi- PDB-7n19: DR3 in complex with Aspergillus nidulans NAD-dependent histone de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n19 | ||||||
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Title | DR3 in complex with Aspergillus nidulans NAD-dependent histone deacetylase hst4 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHCII / T cell | ||||||
Function / homology | Function and homology information 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 / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...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 / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / lumenal side of endoplasmic reticulum 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / adaptive immune response / membrane => GO:0016020 / endosome membrane / lysosome / immune response / Golgi membrane / lysosomal membrane / cell surface / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Wang, Y. / Dai, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Exp.Med. / Year: 2021 Title: CD4+ T cells in the lungs of acute sarcoidosis patients recognize an Aspergillus nidulans epitope. Authors: Greaves, S.A. / Ravindran, A. / Santos, R.G. / Chen, L. / Falta, M.T. / Wang, Y. / Mitchell, A.M. / Atif, S.M. / Mack, D.G. / Tinega, A.N. / Maier, L.A. / Dai, S. / Pinilla, C. / Grunewald, J. / Fontenot, A.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n19.cif.gz | 757.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n19.ent.gz | 517.5 KB | Display | PDB format |
PDBx/mmJSON format | 7n19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n19_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7n19_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7n19_validation.xml.gz | 57.4 KB | Display | |
Data in CIF | 7n19_validation.cif.gz | 79.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/7n19 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/7n19 | HTTPS FTP |
-Related structure data
Related structure data | 1a6aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
-HLA class II histocompatibility ... , 2 types, 8 molecules ADGJBEHK
#1: Protein | Mass: 21084.826 Da / Num. of mol.: 4 / Fragment: UNP residues 26-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01903 #2: Protein | Mass: 22049.486 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1, RP1-93N13.1-001 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5Y7D1 |
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-Protein/peptide , 1 types, 4 molecules CFIL
#3: Protein/peptide | Mass: 1376.502 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Trichoplusia ni (cabbage looper) |
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-Sugars , 2 types, 8 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 270 molecules
#5: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 18% w/v PEG20k, 0.1 M citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50.01 Å / Num. obs: 90818 / % possible obs: 98.53 % / Redundancy: 2 % / Biso Wilson estimate: 55.49 Å2 / CC1/2: 0.994 / Net I/σ(I): 10.86 |
Reflection shell | Resolution: 2.38→2.54 Å / Num. unique obs: 16544 / CC1/2: 0.467 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A6A Resolution: 2.38→48.41 Å / SU ML: 0.4214 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 30.3534 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 59.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→48.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 19.1912610776 Å / Origin y: -0.59085179423 Å / Origin z: 22.6134231241 Å
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Refinement TLS group | Selection details: all |