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- PDB-7na5: Structure of the H2DB-TCR ternary complex with HSF2 melanoma neoa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7na5 | ||||||
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Title | Structure of the H2DB-TCR ternary complex with HSF2 melanoma neoantigen | ||||||
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![]() | IMMUNE SYSTEM / neoantigen / cancer / melanoma / B16 / mouse / H2DB / TCR / TCR-MHC complex / anchor residue mutation / HSF2 | ||||||
Function / homology | ![]() RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / DAP12 interactions / negative regulation of receptor binding ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / 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 / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / sequence-specific double-stranded DNA binding / 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 / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / sequence-specific DNA binding / learning or memory / immune response / Amyloid fiber formation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / protein-containing complex binding / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Finnigan, J. / Patskovska, L. / Newman, J. / Bhardwaj, N. / Krogsgaard, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the TCR-H2DB ternary complex with melanoma HSF2 neoantigen YGFRNVVHI Authors: Patskovsky, Y. / Finnigan, J. / Patskovska, L. / Newman, J. / Bhardwaj, N. / Krogsgaard, 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 | ![]() | 183.2 KB | Display | ![]() |
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PDB format | ![]() | 142 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487 KB | Display | ![]() |
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Full document | ![]() | 494.5 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n9jS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 4 types, 4 molecules ABDE
#1: Protein | Mass: 32601.303 Da / Num. of mol.: 1 / Fragment: UNP residues 25-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 21426.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Protein | Mass: 29788.338 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: 1106.277 Da / Num. of mol.: 1 / Fragment: UNP residues 68-76 / Mutation: K5N / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 3 types, 225 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
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#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.98 % / Description: rods |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M lithium sulfate, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2020 / Details: SI 111 CRYSTAL |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50.01 Å / Num. obs: 35345 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.161 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3783 / CC1/2: 0.45 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 7N9J Resolution: 2.5→50.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.616 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.441 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.5 Å / Shrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.09 Å2 / Biso mean: 51.318 Å2 / Biso min: 24.06 Å2
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Refinement step | Cycle: final / Resolution: 2.5→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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