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Open data
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Basic information
Entry | Database: PDB / ID: 1x7q | ||||||
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Title | Crystal structure of HLA-A*1101 with sars nucleocapsid peptide | ||||||
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![]() | IMMUNE SYSTEM / PEPTIDE-MHC-COMPLEX / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I / MHC-I / HUMAN LEUKOCYTE ANTIGEN / HLA / IMMUNOGLOBULIN FAMILY / SARS | ||||||
Function / homology | ![]() SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / SARS-CoV-1 modulates host translation machinery / 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 / T cell receptor binding / detection of bacterium / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / 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 / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / SARS-CoV-1 activates/modulates innate immune responses / 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 / Interferon alpha/beta signaling / positive regulation of type II interferon production / viral capsid / 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 / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / antibacterial humoral response / T cell differentiation in thymus / protein refolding / host cell Golgi apparatus / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / molecular adaptor activity / learning or memory / host cell perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blicher, T. / Kastrup, J.S. / Buus, S. / Gajhede, M. | ||||||
![]() | ![]() Title: High-resolution structure of HLA-A*1101 in complex with SARS nucleocapsid peptide. Authors: Blicher, T. / Kastrup, J.S. / Buus, S. / Gajhede, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.2 KB | Display | ![]() |
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PDB format | ![]() | 160.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.3 KB | Display | ![]() |
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Full document | ![]() | 481.2 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 37.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hlaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31855.051 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1046.214 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: CHEMICALLY SYNTHESIZED PEPTIDE. THIS SEQUENCE OCCURS NATURALLY IN SARS CORONAVIRUS NUCLEOCAPSID PROTEIN, POSITION 362-370. References: UniProt: P59595 |
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-Non-polymers , 3 types, 584 molecules ![](data/chem/img/SO4.gif)
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#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 5000 MME, 0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 28, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9815 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→36 Å / Num. all: 81898 / Num. obs: 81898 / % possible obs: 100 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 4.84 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 15.94 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 3.94 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.14 / Num. unique all: 4079 / Rsym value: 0.45 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HLA Resolution: 1.45→30 Å / Num. parameters: 34721 / Num. restraintsaints: 42247 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.29 %
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Displacement parameters | Biso mean: 23 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 20 / Occupancy sum hydrogen: 2823.81 / Occupancy sum non hydrogen: 3773.22 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→30 Å
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Refine LS restraints |
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