+Open data
-Basic information
Entry | Database: PDB / ID: 6cqj | |||||||||
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Title | Crystal structure of DR1 presenting the RQ13 peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNE RECEPTOR | |||||||||
Function / homology | Function and homology information host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / 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 / positive regulation of kinase activity / inflammatory response to antigenic stimulus / integrase activity / intermediate filament / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / Binding and entry of HIV virion / negative regulation of inflammatory response to antigenic stimulus / viral life cycle / negative regulation of T cell proliferation / Membrane binding and targetting of GAG proteins / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / ER to Golgi transport vesicle membrane / retroviral ribonuclease H / exoribonuclease H / : / structural constituent of cytoskeleton / exoribonuclease H activity / protein processing / cognition / host multivesicular body / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / RNA-directed DNA polymerase / peptide antigen binding / viral genome integration into host DNA / viral penetration into host nucleus / endocytic vesicle membrane / establishment of integrated proviral latency / antigen processing and presentation of exogenous peptide antigen via MHC class II / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / peptidase activity / T cell receptor signaling pathway / early endosome membrane / viral nucleocapsid / positive regulation of canonical NF-kappaB signal transduction / DNA recombination / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / Hydrolases; Acting on ester bonds / lysosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) HIV-1 M:B_HXB2R (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Farenc, C. / Gras, S. / Rossjohn, J. | |||||||||
Citation | Journal: Sci Immunol / Year: 2018 Title: CD4+T cell-mediated HLA class II cross-restriction in HIV controllers. Authors: Galperin, M. / Farenc, C. / Mukhopadhyay, M. / Jayasinghe, D. / Decroos, A. / Benati, D. / Tan, L.L. / Ciacchi, L. / Reid, H.H. / Rossjohn, J. / Chakrabarti, L.A. / Gras, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cqj.cif.gz | 249.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cqj.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 6cqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/6cqj ftp://data.pdbj.org/pub/pdb/validation_reports/cq/6cqj | HTTPS FTP |
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-Related structure data
Related structure data | 6cphC 6cplC 6cpnC 6cpoC 6cqlC 6cqnC 6cqqC 6cqrC 4mdoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-HLA class II histocompatibility antigen, ... , 2 types, 6 molecules ADGBEH
#1: Protein | Mass: 21185.930 Da / Num. of mol.: 3 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: 22023.611 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: P04229, UniProt: P01911*PLUS |
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-Protein/peptide , 1 types, 3 molecules CFI
#3: Protein/peptide | Mass: 1600.797 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) HIV-1 M:B_HXB2R (virus) / References: UniProt: P04591, UniProt: P04585*PLUS |
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-Sugars , 2 types, 3 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose |
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#6: Sugar |
-Non-polymers , 3 types, 274 molecules
#5: Chemical | ChemComp-PEG / #7: Chemical | #8: 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: 3.08 Å3/Da / Density % sol: 60.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: HEPES pH 7.5, Na acetate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→47.96 Å / Num. obs: 40739 / % possible obs: 98.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 77.15 Å2 / Rpim(I) all: 0.076 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.75→2.86 Å / Num. unique obs: 4564 / Rpim(I) all: 0.417 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MDO Resolution: 2.75→47.96 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.866 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.859 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.334
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Displacement parameters | Biso mean: 52.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.75→47.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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