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Yorodumi- PDB-1hhk: THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hhk | ||||||
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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 symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / 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 ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / regulation of mRNA stability / 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 / SH3 domain binding / 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 / cellular response to lipopolysaccharide / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / 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 / negative regulation of gene expression / innate immune response / focal adhesion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human T-lymphotropic 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: J.Immunol. / Year: 1992 Title: Presentation of Three Different Viral Peptides, Htlv-1 Tax, Hcmv Gb, and Influenza Virus M1, is Determined by Common Structural Features of the Hla-A2.1 Molecule Authors: Utz, U. / Koenig, S. / Coligan, J.E. / Biddison, W.E. #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 | 1hhk.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hhk.ent.gz | 129.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hhk_validation.pdf.gz | 391.3 KB | Display | wwPDB validaton report |
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Full document | 1hhk_full_validation.pdf.gz | 406.9 KB | Display | |
Data in XML | 1hhk_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1hhk_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/1hhk ftp://data.pdbj.org/pub/pdb/validation_reports/hh/1hhk | HTTPS FTP |
-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 17, A 194, A 196, B 48, B 58, D 17, D 194, D 196, E 48, AND E 58 ARE DISORDERED, AND HAVE OCCUPANCIES EQUAL TO ZERO IN THIS ENTRY. 2: RESIDUES PRO A 210, PRO B 32, PRO D 210 AND PRO E 32 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: 1070.280 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human T-lymphotropic virus 1 / Genus: Deltaretrovirus / Species: Primate T-lymphotropic virus 1 / References: UniProt: P14079 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: 2.54 Å3/Da / Density % sol: 51.61 % | ||||||||||||||||||||
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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: 1.8 Å / Lowest resolution: 30 Å / % possible obs: 88 % / Rmerge(I) obs: 0.042 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.262 / Rfactor obs: 0.262 / 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: 25304 / Rfactor obs: 0.262 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.9 |