+Open data
-Basic information
Entry | Database: PDB / ID: 6cpl | |||||||||
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Title | Crystal structure of DR11 presenting the gag293 epitope | |||||||||
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 / 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 ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / 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 / integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / intermediate filament / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / 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 / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / viral life cycle / Membrane binding and targetting of GAG proteins / MHC class II antigen presentation / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / ER to Golgi transport vesicle membrane / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / structural constituent of cytoskeleton / cognition / host multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / viral genome integration into host DNA / RNA-directed DNA polymerase / positive regulation of T cell mediated cytotoxicity / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / host cell / positive regulation of T cell activation / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / Downstream TCR signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / peptidase activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / adaptive immune response / positive regulation of ERK1 and ERK2 cascade Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) HIV-1 M:B_HXB2R (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 | 6cpl.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cpl.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 6cpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cpl_validation.pdf.gz | 786.3 KB | Display | wwPDB validaton report |
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Full document | 6cpl_full_validation.pdf.gz | 790 KB | Display | |
Data in XML | 6cpl_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 6cpl_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/6cpl ftp://data.pdbj.org/pub/pdb/validation_reports/cp/6cpl | HTTPS FTP |
-Related structure data
Related structure data | 6cphC 6cpnC 6cpoC 6cqjC 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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Unit cell |
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-Components
-HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 26014.689 Da / Num. of mol.: 1 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 |
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#2: Protein | Mass: 22246.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: P20039, UniProt: P01911*PLUS |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 2526.758 Da / Num. of mol.: 1 / 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 Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Non-polymers , 4 types, 194 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | #8: Chemical | #9: 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: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris pH 8.5, Ethylene glycol |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.16 Å / Num. obs: 20598 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 58.05 Å2 / Rpim(I) all: 0.052 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.45→2.55 Å / Num. unique obs: 2328 / Rpim(I) all: 0.435 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MDO Resolution: 2.45→45.16 Å / Cor.coef. Fo:Fc: 0.9216 / Cor.coef. Fo:Fc free: 0.9065 / SU R Cruickshank DPI: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.411 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.254
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Displacement parameters | Biso mean: 44.09 Å2
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Refine analyze | Luzzati coordinate error obs: 0.374 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.45→45.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.58 Å / Total num. of bins used: 10
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