+Open data
-Basic information
Entry | Database: PDB / ID: 3bew | ||||||
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Title | 10mer Crystal Structure of chicken MHC class I haplotype B21 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class I / chicken / 10mer / bulge / water cushion / Immune response / Immunoglobulin domain / MHC I / Polymorphism / Secreted / GTP-binding / Microtubule / Nucleotide-binding | ||||||
Function / homology | Function and homology information Intraflagellar transport / Kinesins / Aggrephagy / Post-translational modification: synthesis of GPI-anchored proteins / Transferrin endocytosis and recycling / COPI-dependent Golgi-to-ER retrograde traffic / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...Intraflagellar transport / Kinesins / Aggrephagy / Post-translational modification: synthesis of GPI-anchored proteins / Transferrin endocytosis and recycling / COPI-dependent Golgi-to-ER retrograde traffic / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / 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 / COPI-mediated anterograde transport / microtubule-based process / spindle assembly / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / structural constituent of cytoskeleton / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / microtubule cytoskeleton organization / 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 / 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 / MHC class II protein complex binding / late endosome membrane / mitotic cell cycle / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / microtubule / learning or memory / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / GTPase activity / GTP binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. ...Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. / Marston, D.A. / Shaw, I. / Dunbar, P.R. / Cerundolo, V. / Jones, E.Y. / Kaufman, J. | ||||||
Citation | Journal: Immunity / Year: 2007 Title: Structures of an MHC class I molecule from b21 chickens illustrate promiscuous Peptide binding Authors: Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.-J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. / Marston, D.A. / Shaw, I. / Dunbar, P.R. / Cerundolo, ...Authors: Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.-J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. / Marston, D.A. / Shaw, I. / Dunbar, P.R. / Cerundolo, V. / Jones, E.Y. / Kaufman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bew.cif.gz | 164.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bew.ent.gz | 129.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bew_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 3bew_full_validation.pdf.gz | 477.8 KB | Display | |
Data in XML | 3bew_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 3bew_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/3bew ftp://data.pdbj.org/pub/pdb/validation_reports/be/3bew | HTTPS FTP |
-Related structure data
Related structure data | 3bevSC S: Starting model for refinement C: citing same article (ref.) |
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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: Refine code: 3
NCS ensembles :
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-Components
#1: Protein | Mass: 30930.408 Da / Num. of mol.: 2 / Fragment: UNP residues 1-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Strain: B21 / Gene: BFIV21, B-FIV, BF2 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q95601 #2: Protein | Mass: 11193.601 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Strain: B21 / Gene: B2M / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21611 #3: Protein/peptide | Mass: 1188.308 Da / Num. of mol.: 2 / Fragment: UNP residues 324-333 / Source method: obtained synthetically Details: This sequence occurs naturally in B21 chickens. The peptide was synthesized by solid-phase synthesis. References: UniProt: P09207 #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: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 27% PEG 3350, 0.1M HEPES pH 7.0, 0.1M MgCl2, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9765 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 29, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 39205 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1560 / Rsym value: 0.323 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BEV Resolution: 2.6→29.15 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.854 / SU B: 12.883 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.8 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.337 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→29.15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.657 Å / Total num. of bins used: 20
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