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Yorodumi- PDB-1qew: HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) COMPLEX WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qew | ||||||
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Title | HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) COMPLEX WITH A NONAMERIC PEPTIDE FROM MELANOMA-ASSOCIATED ANTIGEN 3 (RESIDUES 271-279) | ||||||
Components |
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Keywords | COMPLEX (MHC PROTEINTIGEN) / HISTOCOMPATIBILITY ANTIGEN | ||||||
Function / homology | Function and homology information : / : / caspase binding / retina homeostasis / negative regulation of protein processing / regulation of membrane depolarization / 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 ...: / : / caspase binding / retina homeostasis / negative regulation of protein processing / regulation of membrane depolarization / 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 / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / 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 / negative regulation of autophagy / 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 cysteine-type endopeptidase activity involved in apoptotic process / 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 / histone deacetylase binding / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Orth, P. / Alings, C. / Saenger, W. / Ziegler, A. | ||||||
Citation | Journal: To be Published Title: HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) COMPLEX WITH A NONAMERIC PEPTIDE FROM MELANOMA-ASSOCIATED ANTIGEN 3 (RESIDUES 271-279) Authors: Orth, P. / Alings, C. / Saenger, W. / Ziegler, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qew.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qew.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/1qew ftp://data.pdbj.org/pub/pdb/validation_reports/qe/1qew | HTTPS FTP |
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-Related structure data
Related structure data | 1b0gS 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: 31854.203 Da / Num. of mol.: 1 / Fragment: residues 25-299,SWS P01892 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI XA90 / References: UniProt: P01892, UniProt: P04439*PLUS |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: residues 21-199, SWS P01884 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI XA90 / References: UniProt: P01884, UniProt: P61769*PLUS |
#3: Protein/peptide | Mass: 1059.283 Da / Num. of mol.: 1 / Fragment: residues 271-280, SWS P43357 / Source method: isolated from a natural source / Details: SYNTHETIC / Source: (natural) Homo sapiens (human) / References: UniProt: P43357 |
#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: 2.64 Å3/Da / Density % sol: 60 % |
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Crystal grow | pH: 5.6 Details: 20 % POLYETHYLENGLYCOL 8000, SODIUM CITRATE, PH 5.6 |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 22410 / % possible obs: 95.9 % / Redundancy: 2 % / Biso Wilson estimate: 26.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.2→2.3 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.193 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B0G Resolution: 2.2→20 Å / Data cutoff high rms absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.2 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8 /
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Xplor file |
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