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Open data
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Basic information
Entry | Database: PDB / ID: 6cpl | |||||||||
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Title | Crystal structure of DR11 presenting the gag293 epitope | |||||||||
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![]() | IMMUNE SYSTEM / IMMUNE RECEPTOR | |||||||||
Function / homology | ![]() 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 / transport vesicle membrane / intermediate filament / 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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / viral budding via host ESCRT complex / 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 / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / Membrane binding and targetting of GAG proteins / viral life cycle / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Assembly Of The HIV Virion / HIV-1 retropepsin / clathrin-coated endocytic vesicle membrane / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / ER to Golgi transport vesicle membrane / 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 / positive regulation of T cell mediated cytotoxicity / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / RNA-directed DNA polymerase activity / positive regulation of immune response / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / peptidase activity / T cell receptor signaling pathway / symbiont-mediated suppression of host gene expression / early endosome membrane / viral nucleocapsid / DNA recombination / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Farenc, C. / Gras, S. / Rossjohn, J. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786.3 KB | Display | ![]() |
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Full document | ![]() | 790 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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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.) ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 2526.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#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 ![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-SO4 / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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