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Yorodumi- PDB-2clr: THREE DIMENSIONAL STRUCTURE OF A PEPTIDE EXTENDING OUT ONE END OF... -
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-Basic information
Entry | Database: PDB / ID: 2clr | ||||||
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Title | THREE DIMENSIONAL STRUCTURE OF A PEPTIDE EXTENDING OUT ONE END OF A CLASS I MHC BINDING SITE | ||||||
Components |
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Keywords | HISTOCOMPATIBILITY ANTIGEN | ||||||
Function / homology | Function and homology information Calnexin/calreticulin cycle / cytolytic granule / Assembly of Viral Components at the Budding Site / cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus ...Calnexin/calreticulin cycle / cytolytic granule / Assembly of Viral Components at the Budding Site / cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus / intracellular glucocorticoid receptor signaling pathway / endoplasmic reticulum quality control compartment / sequestering of calcium ion / regulation of meiotic nuclear division / response to glycoside / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / hormone binding / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / cardiac muscle cell differentiation / molecular sequestering activity / Scavenging by Class A Receptors / protein maturation by protein folding / Scavenging by Class F Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / response to testosterone / cellular response to lithium ion / smooth endoplasmic reticulum / 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 / protein localization to nucleus / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / negative regulation of neuron differentiation / 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 / positive regulation of cell cycle / positive regulation of phagocytosis / : / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / TAP binding / endocytic vesicle lumen / 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 / protein export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / T cell receptor binding / positive regulation of endothelial cell migration / acrosomal vesicle / 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 / peptide binding / 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 / intracellular calcium ion homeostasis / 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 / cellular response to virus / 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 / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Collins, E.J. / Garboczi, D.N. / Wiley, D.C. | ||||||
Citation | Journal: Nature / Year: 1994 Title: Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Authors: Collins, E.J. / Garboczi, D.N. / Wiley, D.C. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Five Viral Peptide-Hla-A2 Co-Crystals: Simultaneous Space Group Determination and X-Ray Data Collection Authors: Garboczi, D.N. / Madden, D.R. / Wiley, D.C. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Comparison of the P2 Specificity Pocket in Three Human Histocompatibility Antigens: Hla-A(Asterisk)6801, Hla-A(Asterisk)0201, and Hla-B(Asterisk)2705 Authors: Guo, H.-C. / Madden, D.R. / Silver, M.L. / Jardetzky, T.S. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. #3: 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. #4: 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. #5: 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. #6: 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. #7: 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. #8: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2clr.cif.gz | 157 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2clr.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 2clr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/2clr ftp://data.pdbj.org/pub/pdb/validation_reports/cl/2clr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 210 / 2: CIS PROLINE - PRO B 32 / 3: CIS PROLINE - PRO D 210 / 4: CIS PROLINE - PRO E 32 | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES AS FOLLOWS: MTRIX 1: APPLIED TO CHAIN D RESIDUES 1 - 183, APPROXIMATELY GENERATES CHAIN A RESIDUES 1 - 183 MTRIX 1: APPLIED TO CHAIN F RESIDUES 1 - 10, APPROXIMATELY GENERATES CHAIN C RESIDUES 1 - 10 MTRIX 2: APPLIED TO CHAIN D RESIDUES 184 - 275, APPROXIMATELY GENERATES CHAIN A RESIDUES 184 - 275 MTRIX 3: APPLIED TO CHAIN E RESIDUES 1 - 99, APPROXIMATELY GENERATES CHAIN B RESIDUES 1 - 99 |
-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: 1055.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P27797 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.92 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion / PH range low: 6.5 / PH range high: 6.2 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å / Rmerge(I) obs: 0.054 |
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Reflection shell | *PLUS Highest resolution: 2.07 Å / Lowest resolution: 2.16 Å / Rmerge(I) obs: 0.205 |
-Processing
Software |
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Refinement | Resolution: 2→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.299 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |