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Yorodumi- PDB-7n5q: Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n5q | ||||||
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Title | Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Major Histocompatibility complex / MHC / mouse / Influenza A / polymerase acidic protein / H2Db / PA224-233 / Cysteine / mutant | ||||||
Function / homology | Function and homology information cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin 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 / negative regulation of receptor binding ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / endonuclease activity / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / Hydrolases; Acting on ester bonds / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / viral RNA genome replication / focal adhesion / signaling receptor binding / DNA-templated transcription / host cell nucleus / Neutrophil degranulation / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Szeto, C. / Gras, S. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus. Authors: Szeto, C. / Zareie, P. / Wirasinha, R.C. / Zhang, J.B. / Nguyen, A.T. / Riboldi-Tunnicliffe, A. / La Gruta, N.L. / Gras, S. / Daley, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n5q.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n5q.ent.gz | 145.3 KB | Display | PDB format |
PDBx/mmJSON format | 7n5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n5q_validation.pdf.gz | 473.4 KB | Display | wwPDB validaton report |
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Full document | 7n5q_full_validation.pdf.gz | 480.3 KB | Display | |
Data in XML | 7n5q_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 7n5q_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/7n5q ftp://data.pdbj.org/pub/pdb/validation_reports/n5/7n5q | HTTPS FTP |
-Related structure data
Related structure data | 7n4kC 7n5cC 7n5pC 3pqyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules AFBG
#1: Protein | Mass: 32619.275 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P01899 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules CH
#3: Protein/peptide | Mass: 1160.324 Da / Num. of mol.: 2 / Mutation: E4C / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: O89752 |
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-Non-polymers , 3 types, 487 molecules
#4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.1 Å3/Da / Density % sol: 41.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 20% PEG2000, 0.1M KSCN, 2% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.98 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 18, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.76→46.36 Å / Num. obs: 71639 / % possible obs: 97.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.35 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.057 / Rrim(I) all: 0.11 / Net I/σ(I): 9.4 / Num. measured all: 261890 / Scaling rejects: 255 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.7 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PQY Resolution: 1.76→25.32 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.127 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.121
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Displacement parameters | Biso max: 99.08 Å2 / Biso mean: 24.77 Å2 / Biso min: 3.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.76→25.32 Å
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LS refinement shell | Resolution: 1.76→1.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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