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Yorodumi- PDB-3l6f: Structure of MHC class II molecule HLA-DR1 complexed with phospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l6f | ||||||
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Title | Structure of MHC class II molecule HLA-DR1 complexed with phosphopeptide MART-1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PEPTIDE BINDING PROTEIN / MHC class II / HLA-DR1 / phosphopeptide / Disulfide bond / Glycoprotein / Immune response / Membrane / MHC II / Transmembrane / Endoplasmic reticulum / Golgi apparatus / IMMUNE SYSTEM-PEPTIDE BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / 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 / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / trans-Golgi network / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / melanosome / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Li, Y. / Mariuzza, R.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural Basis for the Presentation of Tumor-Associated MHC Class II-Restricted Phosphopeptides to CD4(+) T Cells. Authors: Li, Y. / Depontieu, F.R. / Sidney, J. / Salay, T.M. / Engelhard, V.H. / Hunt, D.F. / Sette, A. / Topalian, S.L. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l6f.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l6f.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 3l6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l6f_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 3l6f_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 3l6f_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 3l6f_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/3l6f ftp://data.pdbj.org/pub/pdb/validation_reports/l6/3l6f | HTTPS FTP |
-Related structure data
Related structure data | 1t5wS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21145.887 Da / Num. of mol.: 1 / Fragment: UNP residues 26-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903 |
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#2: Protein | Mass: 22456.133 Da / Num. of mol.: 1 / Fragment: UNP residues 30-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04229, UniProt: P01911*PLUS |
#3: Protein/peptide | Mass: 1665.710 Da / Num. of mol.: 1 / Fragment: UNP residues 100-114 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.5 Details: 20% (w/v) PEG 8000 and 0.1 M sodium cacodylate, pH 6.5, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→43.22 Å / Num. all: 30437 / Num. obs: 30332 / % possible obs: 100 % / Redundancy: 14.2 % / Rsym value: 0.074 / Net I/σ(I): 51.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.46 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T5W Resolution: 2.1→43.22 Å
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Displacement parameters | Biso mean: 0.043 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→43.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.11 Å /
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