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Yorodumi- PDB-4cvx: COMPLEX OF A B2 CHICKEN MHC CLASS I MOLECULE AND A 9MER CHICKEN P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cvx | ||||||
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Title | COMPLEX OF A B2 CHICKEN MHC CLASS I MOLECULE AND A 9MER CHICKEN PEPTIDE | ||||||
Components |
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Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information 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 / vesicle docking involved in exocytosis / 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 ...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 / vesicle docking involved in exocytosis / 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 / cellular response to iron ion / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / 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 / 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 / positive regulation of immune response / protein transport / 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: 3.3 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 | 4cvx.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cvx.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 4cvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cvx_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 4cvx_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 4cvx_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 4cvx_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvx ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvx | HTTPS FTP |
-Related structure data
Related structure data | 2yezC 4cvzC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 35349.094 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 22-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Description: B2 HAPLOTYPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: O46789 #2: Protein | Mass: 11062.404 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-319 Source method: isolated from a genetically manipulated source 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: 1037.166 Da / Num. of mol.: 2 / Fragment: RESIDUES 314-322 / Source method: obtained synthetically / Details: 9-MER PEPTIDE / Source: (synth.) GALLUS GALLUS (chicken) / References: UniProt: Q5ZJG4 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.51 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.1M MMT BUFFER, PH 7.0, 25% W/V PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.3→75.66 Å / Num. obs: 22882 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.1 | |||||||||||||||
Reflection shell | Resolution: 3.3→3.56 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YF6 2yf6 Resolution: 3.3→75.66 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.879 / SU B: 24.155 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.098 / 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: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.988 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→75.66 Å
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Refine LS restraints |
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