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Yorodumi- PDB-4cvz: COMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 10MER CHICKEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cvz | ||||||
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Title | COMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 10MER CHICKEN PEPTIDE | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / B21 | ||||||
Function / homology | Function and homology information Post-translational modification: synthesis of GPI-anchored proteins / Transferrin endocytosis and recycling / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / Neutrophil degranulation ...Post-translational modification: synthesis of GPI-anchored proteins / Transferrin endocytosis and recycling / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / Neutrophil degranulation / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Chappell, P.E. / Roversi, P. / Harrison, M.C. / Mears, L.E. / Kaufman, J.F. / Lea, S.M. | ||||||
Citation | Journal: Elife / Year: 2015 Title: Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding. Authors: Chappell, P. / Meziane, e.l..K. / Harrison, M. / Magiera, L. / Hermann, C. / Mears, L. / Wrobel, A.G. / Durant, C. / Nielsen, L.L. / Buus, S. / Ternette, N. / Mwangi, W. / Butter, C. / Nair, ...Authors: Chappell, P. / Meziane, e.l..K. / Harrison, M. / Magiera, L. / Hermann, C. / Mears, L. / Wrobel, A.G. / Durant, C. / Nielsen, L.L. / Buus, S. / Ternette, N. / Mwangi, W. / Butter, C. / Nair, V. / Ahyee, T. / Duggleby, R. / Madrigal, A. / Roversi, P. / Lea, S.M. / Kaufman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cvz.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cvz.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 4cvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cvz_validation.pdf.gz | 458.6 KB | Display | wwPDB validaton report |
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Full document | 4cvz_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 4cvz_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 4cvz_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvz ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvz | HTTPS FTP |
-Related structure data
Related structure data | 2yezC 4cvxC 4cw1C 4d0bC 4d0cC 4d0dC 2yf6 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36862.012 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 1-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Description: B21 HAPLOTYPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: Q95601 | ||
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#2: Protein | Mass: 11062.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HEAVY AND LIGHT CHAINS EXPRESSED SEPARATELY IN INCLUSION BODIES AND SUBSEQUENTLY RENATURED TOGETHER IN THE PRESENCE OF PEPTIDE. Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: P21611 | ||
#3: Protein/peptide | Mass: 1329.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GALLUS GALLUS (chicken) | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.93 % / Description: NONE |
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Crystal grow | pH: 5 Details: 0.1M SODIUM ACETATE, PH 5.0, 1.5M AMMONIUM SULFATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Date: Apr 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50.84 Å / Num. obs: 16087 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 44.97 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.39→2.45 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YF6 2yf6 Resolution: 2.39→50.84 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.8704 / SU R Cruickshank DPI: 0.583 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.597 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.284
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Displacement parameters | Biso mean: 30.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.475 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.39→50.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.56 Å / Total num. of bins used: 8
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