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Yorodumi- PDB-2c7u: Conflicting selective forces affect CD8 T-cell receptor contact s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c7u | ||||||
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Title | Conflicting selective forces affect CD8 T-cell receptor contact sites in an HLA-A2 immunodominant HIV epitope. | ||||||
Components |
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Keywords | GLYCOPROTEIN/PEPTIDE / GLYCOPROTEIN-PEPTIDE COMPLEX / MHC / TCR / HLA-A2 / HIV / GLYCOPROTEIN / IMMUNE RESPONSE / MHC I / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / PYRROLIDONE CARBOXYLIC ACID / AIDS | ||||||
Function / homology | Function and homology information T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) HUMAN IMMUNODEFICIENCY VIRUS 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.38 Å | ||||||
Authors | Iversen, A.K. / Stewart-Jones, G. / Learn, G.H. / Christie, N. / Sylvester-Hviid, C. / Armitage, A.E. / Kaul, R. / Beattie, T. / Lee, J.K. / Li, Y. ...Iversen, A.K. / Stewart-Jones, G. / Learn, G.H. / Christie, N. / Sylvester-Hviid, C. / Armitage, A.E. / Kaul, R. / Beattie, T. / Lee, J.K. / Li, Y. / Chotiyarnwong, P. / Dong, T. / Xu, X. / Luscher, M.A. / MacDonald, K. / Ullum, H. / Klarlund-Pedersen, B. / Skinhoj, P. / Fugger, J.L. / Buus, S. / Mullins, J.I. / Jones, E.Y. / van der Merwe, P.A. / McMichael, A.J. | ||||||
Citation | Journal: Nat.Immunol. / Year: 2006 Title: Conflicting Selective Forces Affect T Cell Receptor Contacts in an Immunodominant Human Immunodeficiency Virus Epitope. Authors: Iversen, A.K. / Stewart-Jones, G. / Learn, G.H. / Christie, N. / Sylvester-Hviid, C. / Armitage, A.E. / Kaul, R. / Beattie, T. / Lee, J.K. / Li, Y. / Chotiyarnwong, P. / Dong, T. / Xu, X. / ...Authors: Iversen, A.K. / Stewart-Jones, G. / Learn, G.H. / Christie, N. / Sylvester-Hviid, C. / Armitage, A.E. / Kaul, R. / Beattie, T. / Lee, J.K. / Li, Y. / Chotiyarnwong, P. / Dong, T. / Xu, X. / Luscher, M.A. / Macdonald, K. / Ullum, H. / Klarlund-Pedersen, B. / Skinhoj, P. / Fugger, L. / Buus, S. / Mullins, J.I. / Jones, E.Y. / Van Der Merwe, P.A. / Mcmichael, A.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c7u.cif.gz | 166.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c7u.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 2c7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c7u_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 2c7u_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 2c7u_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 2c7u_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/2c7u ftp://data.pdbj.org/pub/pdb/validation_reports/c7/2c7u | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P61769 #3: Protein/peptide | Mass: 977.155 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-15 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS 1 / References: UniProt: O11822 #4: Water | ChemComp-HOH / | Compound details | INVOLVED IN THE PRESENTATI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.37 % |
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Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.977 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 23, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 138420 / % possible obs: 96.8 % / Observed criterion σ(I): 0.9 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 2.38→81.38 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.881 / SU B: 26.462 / SU ML: 0.326 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→81.38 Å
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