+Open data
-Basic information
Entry | Database: PDB / ID: 2xpg | ||||||
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Title | Crystal structure of a MHC class I-peptide complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / AUTOIMMUNITY / MULTIPLE SCLEROSIS | ||||||
Function / homology | Function and homology information structural constituent of myelin sheath / axon ensheathment / central nervous system myelination / astrocyte development / long-chain fatty acid biosynthetic process / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation ...structural constituent of myelin sheath / axon ensheathment / central nervous system myelination / astrocyte development / long-chain fatty acid biosynthetic process / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / axon development / 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 / 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 / detection of bacterium / T cell receptor binding / substantia nigra development / 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 / 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 / lumenal side of endoplasmic reticulum membrane / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / neuron projection development / 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 / positive regulation of type II interferon production / Interferon alpha/beta signaling / 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 / myelin sheath / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / chemical synaptic transmission / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / defense response to Gram-positive bacterium / inflammatory response / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | McMahon, R.M. / Friis, L. / Siebold, C. / Friese, M.A. / Fugger, L. / Jones, E.Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Structure of Hla-A0301 in Complex with a Peptide of Proteolipid Protein: Insights Into the Role of Hla-A Alleles in Susceptibility to Multiple Sclerosis Authors: Mcmahon, R.M. / Friis, L. / Siebold, C. / Friese, M.A. / Fugger, L. / 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 | 2xpg.cif.gz | 168.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xpg.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/2xpg ftp://data.pdbj.org/pub/pdb/validation_reports/xp/2xpg | HTTPS FTP |
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-Related structure data
Related structure data | 1duzS S: Starting model for refinement |
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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: 31628.838 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 25-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: P04439 |
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#2: Protein | Mass: 11574.885 Da / Num. of mol.: 1 / Fragment: BETA2-MICROGLOBULIN FORM PI 5.3, RESIDUES 22-118 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1130.333 Da / Num. of mol.: 1 / Fragment: RESIDUES 45-53 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P60201 |
#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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.1 M BIS-TRIS-PROPANE, PH 8.0, 0.2 M NA/K PHOSPHATE, 20% (V/V) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9699 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 14030 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 34.93 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DUZ Resolution: 2.6→19.75 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 25.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.3 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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