+Open data
-Basic information
Entry | Database: PDB / ID: 1x7q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of HLA-A*1101 with sars nucleocapsid peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / PEPTIDE-MHC-COMPLEX / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I / MHC-I / HUMAN LEUKOCYTE ANTIGEN / HLA / IMMUNOGLOBULIN FAMILY / SARS | ||||||
Function / homology | Function and homology information 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 / SARS-CoV-1 modulates host translation machinery / 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 ...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 / SARS-CoV-1 modulates host translation machinery / 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 / Attachment and Entry / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 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 / 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 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 / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / SARS-CoV-1 activates/modulates innate immune responses / viral capsid / 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 / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / host cell Golgi apparatus / early endosome membrane / protein homotetramerization / viral nucleocapsid / intracellular iron ion homeostasis / amyloid fibril formation / host cell perinuclear region of cytoplasm / learning or memory / molecular adaptor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Blicher, T. / Kastrup, J.S. / Buus, S. / Gajhede, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1x7q.cif.gz | 202.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1x7q.ent.gz | 160.9 KB | Display | PDB format |
PDBx/mmJSON format | 1x7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/1x7q ftp://data.pdbj.org/pub/pdb/validation_reports/x7/1x7q | HTTPS FTP |
---|
-Related structure data
Related structure data | 1hlaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13746, UniProt: P04439*PLUS |
---|---|
#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61769 |
-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 |
---|
-Non-polymers , 3 types, 584 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.5 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9815 / Wavelength: 0.9815 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 %
| |||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|