+Open data
-Basic information
Entry | Database: PDB / ID: 3dmm | ||||||
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Title | Crystal structure of the CD8 alpha beta/H-2Dd complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T cell co-receptor CD8ab MHC complex / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Secreted / Envelope protein / Alternative splicing / Polymorphism | ||||||
Function / homology | Function and homology information cytotoxic T cell differentiation / T cell mediated immunity / 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 / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...cytotoxic T cell differentiation / T cell mediated immunity / 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 / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / 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 / calcium-mediated signaling / lumenal side of endoplasmic reticulum membrane / 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 / 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 / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / defense response to virus / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / protein kinase binding / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Wang, R. / Natarajan, K. / Margulies, D.H. | ||||||
Citation | Journal: J.Immunol. / Year: 2009 Title: Structural basis of the CD8alphabeta/MHC class i interaction: focused recognition orients CD8beta to a T cell proximal position. Authors: Wang, R. / Natarajan, K. / Margulies, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dmm.cif.gz | 142.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dmm.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dmm_validation.pdf.gz | 466.7 KB | Display | wwPDB validaton report |
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Full document | 3dmm_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 3dmm_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 3dmm_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/3dmm ftp://data.pdbj.org/pub/pdb/validation_reports/dm/3dmm | HTTPS FTP |
-Related structure data
Related structure data | 3ecbC 1qo3S 2atpS 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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1 |
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Unit cell |
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Details | THE ASYMMETRIC UNIT IS THE BIOLOGICAL COMPLEX, CONSISTING OF CHAINS A,B,P,C,D. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32007.609 Da / Num. of mol.: 1 / Fragment: Alpha-1,2,3 regions: Residues 26-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P01900 |
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#2: Protein | Mass: 11791.545 Da / Num. of mol.: 1 / Fragment: Residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XJ8, UniProt: P01887*PLUS |
-T-cell surface glycoprotein CD8 ... , 2 types, 2 molecules CD
#4: Protein | Mass: 18361.881 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain: Residues 28-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8a, Lyt-2, Lyt2 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P01731 |
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#5: Protein | Mass: 16883.535 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain: Residues 22-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8b, Cd8b1, Ly-3, Lyt-3, Lyt3 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P10300 |
-Protein/peptide / Non-polymers , 2 types, 38 molecules P
#3: Protein/peptide | Mass: 1075.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide |
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#6: 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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 12% PEG 3000, 0.05M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 22842 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.45 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.6 / % possible all: 76.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1QO3, 2ATP Resolution: 2.6→43.32 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 92554.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT / Bsol: 63.66 Å2 / ksol: 0.409086 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→43.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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