+Open data
-Basic information
Entry | Database: PDB / ID: 6bj3 | ||||||
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Title | TCR55 in complex with HIV(Pol448-456)/HLA-B35 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / non-agonist / complex | ||||||
Function / homology | Function and homology information regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / TAP binding / protection from natural killer cell mediated cytotoxicity / Binding and entry of HIV virion / detection of bacterium / viral life cycle / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / cellular response to iron(III) ion / Assembly Of The HIV Virion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / retroviral ribonuclease H / negative regulation of forebrain neuron differentiation / exoribonuclease H / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / exoribonuclease H activity / response to molecule of bacterial origin / MHC class I peptide loading complex / Budding and maturation of HIV virion / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / host multivesicular body / MHC class I protein complex / protein processing / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / viral genome integration into host DNA / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / MHC class II protein complex / cellular response to nicotine / symbiont-mediated suppression of host gene expression / specific granule lumen / viral penetration into host nucleus / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / RNA-directed DNA polymerase activity / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / RNA-DNA hybrid ribonuclease activity / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / sensory perception of smell / host cell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / peptidase activity / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å | ||||||
Authors | Jude, K.M. / Sibener, L.V. / Garcia, K.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2018 Title: Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding. Authors: Sibener, L.V. / Fernandes, R.A. / Kolawole, E.M. / Carbone, C.B. / Liu, F. / McAffee, D. / Birnbaum, M.E. / Yang, X. / Su, L.F. / Yu, W. / Dong, S. / Gee, M.H. / Jude, K.M. / Davis, M.M. / ...Authors: Sibener, L.V. / Fernandes, R.A. / Kolawole, E.M. / Carbone, C.B. / Liu, F. / McAffee, D. / Birnbaum, M.E. / Yang, X. / Su, L.F. / Yu, W. / Dong, S. / Gee, M.H. / Jude, K.M. / Davis, M.M. / Groves, J.T. / Goddard III, W.A. / Heath, J.R. / Evavold, B.D. / Vale, R.D. / Garcia, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bj3.cif.gz | 355.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bj3.ent.gz | 289 KB | Display | PDB format |
PDBx/mmJSON format | 6bj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bj3_validation.pdf.gz | 473.3 KB | Display | wwPDB validaton report |
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Full document | 6bj3_full_validation.pdf.gz | 477.6 KB | Display | |
Data in XML | 6bj3_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 6bj3_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/6bj3 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/6bj3 | HTTPS FTP |
-Related structure data
Related structure data | 6bj2C 6bj8C 1a1nS 4lfhS 4pj5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/519 / Data set type: diffraction image data / Details: SBGrid Data Bank |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABDH
#1: Protein | Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30685, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769 |
#3: Protein | Mass: 22890.752 Da / Num. of mol.: 1 / Mutation: T161C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IRV4 |
#4: Protein | Mass: 27390.535 Da / Num. of mol.: 1 / Mutation: A187C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: K7N5M4 |
-Protein/peptide , 1 types, 1 molecules C
#5: Protein/peptide | Mass: 1014.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS |
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-Non-polymers , 3 types, 372 molecules
#6: Chemical | #7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 2.87 Å3/Da / Density % sol: 57.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: PEG4000, 0.1 M sodium cacodylate, pH 6.0, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99995 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99995 Å / Relative weight: 1 |
Reflection | Resolution: 1.898→50 Å / Num. obs: 83485 / % possible obs: 97.79 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.9 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.1382 / Rpim(I) all: 0.0853 / Rrim(I) all: 0.1628 / Net I/σ(I): 4.67 |
Reflection shell | Resolution: 1.898→1.966 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.313 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 7910 / CC1/2: 0.406 / Rpim(I) all: 0.8382 / Rrim(I) all: 1.563 / % possible all: 92.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1A1N, 4LFH, 4PJ5 Resolution: 1.898→48.094 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.898→48.094 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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