+Open data
-Basic information
Entry | Database: PDB / ID: 6apn | ||||||||||||||||||||
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Title | HLA-A*0201 single chain trimer with HPV.16 E7 peptide LLMGTLGIV | ||||||||||||||||||||
Components | Beta-2-microglobulin--HLA-A*Keywords | IMMUNE SYSTEM / HLA class I / HLA-A*02 / HPV | Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / : / positive regulation of actin filament polymerization / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / : / positive regulation of actin filament polymerization / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / 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 / viral process / T cell receptor binding / 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 / 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 / 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 / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / 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 / DNA-binding transcription factor binding / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / DNA-binding transcription factor activity / Amyloid fiber formation / lysosomal membrane / protein domain specific binding / external side of plasma membrane Similarity search - Function Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | Authors | Finton, K.A.K. | Citation | Journal: To Be Published | Title: Effects of HLA single chain trimer design on peptide presentation and stability Authors: Finton, K.A.K. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6apn.cif.gz | 312.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6apn.ent.gz | 254.1 KB | Display | PDB format |
PDBx/mmJSON format | 6apn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/6apn ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6apn | HTTPS FTP |
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-Related structure data
Related structure data | 6e1iC 3mrkS 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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Unit cell |
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-Components
#1: Protein | Mass: 50091.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P, HLA-A, HLAA / Production host: Homo sapiens (human) References: UniProt: P61769, UniProt: P01892, UniProt: P03129*PLUS #2: Water | ChemComp-HOH / | Sequence details | chimera composition: HPV.16 E7 peptide LLMGTLGIV - LINKER -- Beta-2-microglobulin -- LINKER -- HLA- ...chimera composition: HPV.16 E7 peptide LLMGTLGIV - LINKER -- Beta-2-microglobulin -- LINKER -- HLA-A*0201 -- Expression tag | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6,5, 25% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→50.01 Å / Num. obs: 37686 / % possible obs: 90.7 % / Redundancy: 3.1 % / Net I/σ(I): 12.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MRK Resolution: 2.22→50.01 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.294 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.033 Å2
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Refinement step | Cycle: 1 / Resolution: 2.22→50.01 Å
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