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Yorodumi- PDB-2hla: SPECIFICITY POCKETS FOR THE SIDE CHAINS OF PEPTIDE ANTIGENS IN HL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hla | ||||||
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Title | SPECIFICITY POCKETS FOR THE SIDE CHAINS OF PEPTIDE ANTIGENS IN HLA-AW68 | ||||||
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 / 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 / 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 / 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 / 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 / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / 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 / 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 / positive regulation of type II interferon production / sensory perception of smell / 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 / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / 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) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Garrett, T.P.J. / Saper, M.A. / Wiley, D.C. | ||||||
Citation | Journal: Nature / Year: 1989 Title: Specificity pockets for the side chains of peptide antigens in HLA-Aw68. Authors: Garrett, T.P. / Saper, M.A. / Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C. #2: 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. #3: 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. #4: 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 SHEET 2 HAS A BETA BULGE AT RESIDUE SER A 207 AND SHEET 4 HAS A BETA BULGE AT RESIDUE GLY B ...SHEET SHEET 2 HAS A BETA BULGE AT RESIDUE SER A 207 AND SHEET 4 HAS A BETA BULGE AT RESIDUE GLY B 29. ADDITIONALLY, IN EACH OF SHEETS 2 AND 4, STRAND 4 CONTAINS AN EXTRA RESIDUE WHICH DISRUPTS THE HYDROGEN BONDING PATTERN. THIS IS REPRESENTED BY PRESENTING THE SHEETS TWICE (DESIGNATED SHEETS S2A, S2B AND S4A, S4B RESPECTIVELY) WHERE THE TWO REPRESENTATIONS DIFFER IN THEIR FIRST AND LAST STRANDS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hla.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hla.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/2hla ftp://data.pdbj.org/pub/pdb/validation_reports/hl/2hla | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: FOR RESIDUES GLY A 1, LYS A 268, PRO A 269 AND LEU A 270 THERE IS NO INTERPRETABLE DENSITY FOR ATOMS WITH AN OCCUPANCY OF 0.01. 2: RESIDUES PRO A 210 AND PRO B 32 ARE CIS PROLINES. |
-Components
#1: Protein | Mass: 31151.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01891, UniProt: P04439*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61769 |
#3: Water | ChemComp-HOH / |
Compound details | RESIDUE ASN A 86 IS THE CARBOHYDRATE ATTACHMENT SITE. NO CARBOHYDRATE COORDINATES HAVE BEEN ...RESIDUE ASN A 86 IS THE CARBOHYDRA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.39 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion / Details: referred to J.Mol.Biol. 186.205-210 1985 / PH range low: 6.5 / PH range high: 6.2 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.6→6 Å / Rfactor Rwork: 0.173 Details: FOR RESIDUES GLY A 1, LYS A 268, PRO A 269 AND LEU A 270 THERE IS NO INTERPRETABLE DENSITY FOR ATOMS WITH AN OCCUPANCY OF 0.01. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 6 Å / σ(I): 1 / Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.2 |