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Yorodumi- PDB-1a1m: MHC CLASS I MOLECULE B*5301 COMPLEXED WITH PEPTIDE TPYDINQML FROM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a1m | ||||||
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Title | MHC CLASS I MOLECULE B*5301 COMPLEXED WITH PEPTIDE TPYDINQML FROM GAG PROTEIN OF HIV2 | ||||||
Components |
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Keywords | COMPLEX (ANTIGEN/PEPTIDE) / MAJOR HISTOCOMPATIBILITY ANTIGEN / MHC / HLA / HLA-B53 / HIV / COMPLEX (ANTIGEN-PEPTIDE) / COMPLEX (ANTIGEN-PEPTIDE) complex | ||||||
Function / homology | Function and homology information regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Smith, K.J. / Reid, S.W. / Harlos, K. / Mcmichael, A.J. / Stuart, D.I. / Bell, J.I. / Jones, E.Y. | ||||||
Citation | Journal: Immunity / Year: 1996 Title: Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53. Authors: Smith, K.J. / Reid, S.W. / Harlos, K. / McMichael, A.J. / Stuart, D.I. / Bell, J.I. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a1m.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a1m.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a1m_validation.pdf.gz | 376.5 KB | Display | wwPDB validaton report |
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Full document | 1a1m_full_validation.pdf.gz | 382.6 KB | Display | |
Data in XML | 1a1m_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1a1m_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a1m ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a1m | HTTPS FTP |
-Related structure data
Related structure data | 1a1oC 1hsaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32282.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: GAG / Plasmid: BL21 / Gene (production host): GAG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P30491, UniProt: P01889*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) / Cell line: BL21 / Gene: GAG / Plasmid: BL21 / Gene (production host): GAG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1094.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TPYDINQML FROM HIV-2 GAG PROTEIN / Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 18% PEG8000 0.1M SODIUM CACODYLATE PH6.5 0.2M CALCIUM ACETATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.97 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 9, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 27424 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HSA Resolution: 2.3→15 Å
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Displacement parameters | Biso mean: 26.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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