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Yorodumi- PDB-1hhj: THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARIS... -
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-Basic information
Entry | Database: PDB / ID: 1hhj | ||||||
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Title | THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2 | ||||||
Components |
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Keywords | HISTOCOMPATIBILITY ANTIGEN | ||||||
Function / homology | Function and homology information T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / : / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / retroviral ribonuclease H / exoribonuclease H / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / : / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / host multivesicular body / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / DNA integration / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / RNA-directed DNA polymerase / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / positive regulation of type II interferon production / sensory perception of smell / RNA-DNA hybrid ribonuclease activity / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / DNA recombination / intracellular iron ion homeostasis / amyloid fibril formation / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Madden, D.R. / Garboczi, D.N. / Wiley, D.C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1993 Title: The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2. Authors: Madden, D.R. / Garboczi, D.N. / Wiley, D.C. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Hla-A2-Peptide Complexes: Refolding and Crystallization of Molecules Expressed in Escherichia Coli and Complexed with Single Antigenic Peptides Authors: Garboczi, D.N. / Hung, D.T. / Wiley, D.C. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: An Optimal Viral Peptide Recognized by Cd8+ T Cells Binds Very Tightly to the Restricting Class I Major Histocompatibility Complex Protein on Intact Cells But not to the Purified Class I Protein Authors: Tsomides, T.J. / Walker, B.D. / Eisen, H.N. #3: Journal: Cell(Cambridge,Mass.) / Year: 1992 Title: The Three-Dimensional Structure of Hla-B27 at 2.1 Angstroms Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. #4: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution Authors: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C. #5: Journal: Nature / Year: 1987 Title: Structure of the Human Class I Histocompatibility Antigen, Hla-A2 Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C. #6: Journal: Nature / Year: 1987 Title: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C. #7: Journal: J.Mol.Biol. / Year: 1985 Title: Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes Authors: Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C. | ||||||
History |
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Remark 700 | SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE ...SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE SHEETS TWICE (DESIGNATED SHEETS SB1, SB2 AND SD1, SD2 RESPECTIVELY) WHERE THE TWO REPRESENTATIONS DIFFER IN THEIR LAST STRAND. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hhj.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hhj.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/1hhj ftp://data.pdbj.org/pub/pdb/validation_reports/hh/1hhj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: SIDE CHAIN ATOMS OF A 176, A 194, A 196, A 223, A 268, B 58, D 176, D 194, D 223, D 268, E 58, E 74 ARE DISORDERED, AND HAVE OCCUPANCIES EQUAL TO ZERO IN THIS ENTRY. 2: RESIDUES PRO A 210, PRO B 32, PRO C 5, PRO D 210, PRO E 32, PRO F 5 ARE CIS PROLINES. 3: ESCHERICHIA COLI EXPRESSED BETA-2 MICROGLOBULIN CONTAINS AN N-TERMINAL METHIONINE, IDENTIFIED HERE BY RESIDUE NUMBER 0. |
-Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-2-MICROGLOBULIN / Production host: Escherichia coli (E. coli) / 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) / Gene: BETA-2-MICROGLOBULIN / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 #3: Protein/peptide | Mass: 993.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P04588 Compound details | SECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER ...SECONDARY STRUCTURE SPECIFICAT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % possible obs: 88 % / Rmerge(I) obs: 0.046 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.278 / Rfactor obs: 0.278 / Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 6 Å / Num. reflection obs: 22064 / Rfactor obs: 0.278 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3 |