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Open data
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Basic information
Entry | Database: PDB / ID: 7n2p | ||||||
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Title | AS4.3-RNASEH2b-HLA*B27 | ||||||
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![]() | IMMUNE SYSTEM / TCR MHC HLA-B27 | ||||||
Function / homology | ![]() 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 ...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 / 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 / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, X. / Jude, K.M. / Garcia, K.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Authors: Yang, X. / Garner, L.I. / Zvyagin, I.V. / Paley, M.A. / Komech, E.A. / Jude, K.M. / Zhao, X. / Fernandes, R.A. / Hassman, L.M. / Paley, G.L. / Savvides, C.S. / Brackenridge, S. / Quastel, M. ...Authors: Yang, X. / Garner, L.I. / Zvyagin, I.V. / Paley, M.A. / Komech, E.A. / Jude, K.M. / Zhao, X. / Fernandes, R.A. / Hassman, L.M. / Paley, G.L. / Savvides, C.S. / Brackenridge, S. / Quastel, M.N. / Chudakov, D.M. / Bowness, P. / Yokoyama, W.M. / McMichael, A.J. / Gillespie, G.M. / Garcia, K.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 412.2 KB | Display | ![]() |
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PDB format | ![]() | 280.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 511.7 KB | Display | ![]() |
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Full document | ![]() | 523.4 KB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 41.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n2nC ![]() 7n2oC ![]() 7n2qC ![]() 7n2rC ![]() 7n2sC ![]() 8cx4C ![]() 1jgeS ![]() 5ksbS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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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: 32086.250 Da / Num. of mol.: 1 / Mutation: C67S 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.) ![]() ![]() ![]() |
-AS4.3 T cell receptor ... , 2 types, 2 molecules DF
#4: Protein | Mass: 22399.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#5: Protein | Mass: 27313.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein/peptide / Sugars , 2 types, 5 molecules C![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Protein/peptide | Mass: 957.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#7: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 67 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-SO4 / | #9: 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: 2.3 Å3/Da / Density % sol: 46.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 with 0.2M Magnesium formate dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.046 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47 Å / Num. obs: 32459 / % possible obs: 99.12 % / Redundancy: 4.4 % / Biso Wilson estimate: 44.51 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rpim(I) all: 0.1298 / Rrim(I) all: 0.2782 / Rsym value: 0.2445 / Net I/σ(I): 5.88 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 0.79 / Num. unique obs: 3146 / CC1/2: 0.318 / CC star: 0.694 / Rpim(I) all: 1.123 / Rrim(I) all: 2.427 / Rsym value: 2.139 / % possible all: 97.94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KSB, 1JGE Resolution: 2.5→47 Å / SU ML: 0.458 / Cross valid method: FREE R-VALUE / Phase error: 32.1973 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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