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Open data
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Basic information
Entry | Database: PDB / ID: 1qlf | ||||||
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Title | MHC CLASS I H-2DB COMPLEXED WITH GLYCOPEPTIDE K3G | ||||||
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![]() | IMMUNE SYSTEM/PEPTIDE / MURINE CLASS I MHC-PEPTIDE COMPLEX / MHC / GLYCOPEPTIDE / ANTIGEN / HISTOCOMPATIBILITY / IMMUNOLOGY / IMMUNE SYSTEM-PEPTIDE complex | ||||||
Function / homology | ![]() : / : / regulation of membrane depolarization / retina homeostasis / helical viral capsid / 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 ...: / : / regulation of membrane depolarization / retina homeostasis / helical viral capsid / 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / antibacterial humoral response / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / viral nucleocapsid / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / ribonucleoprotein complex / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tormo, J. / Jones, E.Y. | ||||||
![]() | ![]() Title: Crystal Structures of Two H-2Db/Glycopeptide Complexes Suggest a Molecular Basis for Ctl Cross-Reactivity Authors: Glithero, A. / Tormo, J. / Haurum, J.S. / Arsequell, G. / Valencia, G. / Edwards, J. / Springer, S. / Townsend, A. / Pao, Y.-L. / Wormald, M. / Dwek, R.A. / Jones, E.Y. / Elliot, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 72.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419 KB | Display | ![]() |
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Full document | ![]() | 426.4 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ce6SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 32087.703 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Details: FORMS HETEROTRIMER WITH CHAIN B (BETA-2-MICROGLOBULIN) AND CHAIN C (PEPTIDE ANTIGEN) Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: MHC ASSOCIATED LIGHT CHAIN Source method: isolated from a genetically manipulated source Details: FORMS HETEROTRIMER WITH CHAIN A AND CHAIN C / Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide / Sugars , 2 types, 2 molecules C![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Protein/peptide | Mass: 979.086 Da / Num. of mol.: 1 Fragment: H-2DB-BOUND GLYCOPEPTIDE FROM NUCLEOCAPSID PROTEIN Source method: obtained synthetically Details: PEPTIDE DERIVED FROM SENDAI VIRUS NUCLEOPROTEIN RESIDUES 324-332, GLY327 HAS BEEN REPLACED BY AN O-GLCNAC SUBSTITUTED SERINE Source: (synth.) ![]() |
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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 163 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
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#4: Chemical | #5: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→10 Å / Num. obs: 14363 / % possible obs: 97 % / Biso Wilson estimate: 39.3 Å2 / Rsym value: 0.06 |
Reflection shell | Resolution: 2.65→2.73 Å / Rsym value: 0.17 / % possible all: 95.1 |
Reflection | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 95.1 % / Rmerge(I) obs: 0.176 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CE6 Resolution: 2.65→20 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE CARBOHYDRATE ATTACHED TO THE GLYCOPEPTIDE IS DISORDERED. ONLY ONE OF THE TWO MAJOR CONFORMATIONS HAS BEEN MODELLED WITH HALF OCCUPANCY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.7963 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.74 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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