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Yorodumi- PDB-4h25: TCR interaction with peptide mimics of nickel offers structure in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h25 | |||||||||
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Title | TCR interaction with peptide mimics of nickel offers structure insights to nickel contact allergy | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / protein protein complex / immunoglobulin fold / antigen presentation / TCR / cell surface | |||||||||
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 / lumenal side of endoplasmic reticulum membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / 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 / adaptive immune response / lysosome / endosome membrane / immune response / lysosomal membrane / Golgi membrane / cell surface / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Kappler, J.W. / Yin, L. / Dai, S. / Marrack, P. / Crawford, F. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: T-cell receptor (TCR) interaction with peptides that mimic nickel offers insight into nickel contact allergy. Authors: Yin, L. / Crawford, F. / Marrack, P. / Kappler, J.W. / Dai, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h25.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h25.ent.gz | 145.5 KB | Display | PDB format |
PDBx/mmJSON format | 4h25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h25_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 4h25_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4h25_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 4h25_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/4h25 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/4h25 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 20913.568 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: homo sapiens (human) / References: UniProt: P01903 #2: Protein | Mass: 21936.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB3 / Production host: homo sapiens (human) / References: UniProt: B8YAC7 |
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-Protein/peptide / Sugars , 2 types, 8 molecules CF
#3: Protein/peptide | Mass: 2490.026 Da / Num. of mol.: 2 / Source method: obtained synthetically #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 |
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-Non-polymers , 2 types, 379 molecules
#5: Chemical | ChemComp-IPA / #6: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 16% PEG4000, 100mM Tris-HCL, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 48623 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THE RFREE VALUE PROVIDED BY AUTHORS CAN NOT BE REPRODUCED BASED ON THE RFREE FLAGS PROVIDED BY AUTHORS Resolution: 2.2→40 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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