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- PDB-2clv: MHC Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With bet... -
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Basic information
Entry | Database: PDB / ID: 2clv | ||||||
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Title | MHC Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and pBM8 peptide | ||||||
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![]() | IMMUNE SYSTEM / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / GLYCOPROTEIN / TRANSMEMBRANE / ALLOREACTIVITY / MHC I / H-2KBM8 / MEMBRANE / CLASS I MHC / POLYMORPHISM | ||||||
Function / homology | ![]() mRNA Splicing - Major Pathway / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / antigen processing and presentation of exogenous peptide antigen via MHC class I ...mRNA Splicing - Major Pathway / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / spliceosomal complex / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / mRNA splicing, via spliceosome / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / 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 / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / positive regulation of apoptotic process / external side of plasma membrane / lysosomal membrane / signaling receptor binding / mRNA binding / protein-containing complex binding / apoptotic process / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mazza, C. / Auphan-Anezin, N. / Guimezanes, A. / Barrett-Wilt, G.A. / Montero-Julian, F. / Roussel, A. / Hunt, D.F. / Schmitt-Verhulst, A.M. / Malissen, B. | ||||||
![]() | ![]() Title: Distinct orientation of the alloreactive monoclonal CD8 T cell activation program by three different peptide/MHC complexes. Authors: Auphan-Anezin, N. / Mazza, C. / Guimezanes, A. / Barrett-Wilt, G.A. / Montero-Julian, F. / Roussel, A. / Hunt, D.F. / Malissen, B. / Schmitt-Verhulst, A.M. #1: ![]() Title: Cdr3 Loop Flexibility Contributes to the Degeneracy of Tcr Recognition Authors: Reiser, J.B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearney, A. / Van Der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180 KB | Display | ![]() |
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PDB format | ![]() | 143.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2clzC ![]() 1nanS 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
#1: Protein | Mass: 32078.799 Da / Num. of mol.: 2 Fragment: EXTRACELLULAR DOMAINS (ALPHA1, ALPHA2, ALPHA3), RESIDUES 22-300 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1037.082 Da / Num. of mol.: 2 / Fragment: RESIDUES 189-196 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 22 TO PHE ENGINEERED RESIDUE IN CHAIN A, MET 23 TO ILE ...ENGINEERED | Sequence details | THE Y22F, M23I, E24S, D30N QUADRUPLE MUTANT IS CALLED BM8, A NATURALLY OCCURING MUTANT IN MICE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | pH: 6.3 / Details: 14% PEG 10000, 100 MM MES PH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 78205 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1NAN Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.36 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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