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- PDB-2ve6: Crystal structure of a Murine MHC class I H2-Db molecule in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ve6 | |||||||||
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Title | Crystal structure of a Murine MHC class I H2-Db molecule in complex with a photocleavable peptide | |||||||||
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![]() | IMMUNE SYSTEM / PHOTOCLEAVABLE PEPTIDE / AUXILIARY ANCHORING RESIDUE / GLYCOPROTEIN / TRANSMEMBRANE / PEPTIDE LOADING / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / MHC / SEV9 / MHC I / MEMBRANE / SECRETED | |||||||||
Function / homology | ![]() 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 / 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 ...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 / 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 / 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 / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Grotenbreg, G.M. / Roan, N.R. / Guillen, E. / Meijers, R. / Wang, J.H. / Bell, G.W. / Starnbach, M.N. / Ploegh, H.L. | |||||||||
![]() | ![]() Title: Discovery of Cd8+ T Cell Epitopes in Chlamydia Trachomatis Infection Through Use of Caged Class I Mhc Tetramers. Authors: Grotenbreg, G.M. / Roan, N.R. / Guillen, E. / Meijers, R. / Wang, J.H. / Bell, G.W. / Starnbach, M.N. / Ploegh, H.L. | |||||||||
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 | ![]() | 315.9 KB | Display | ![]() |
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PDB format | ![]() | 258.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.6 KB | Display | ![]() |
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Full document | ![]() | 522.4 KB | Display | |
Data in XML | ![]() | 55.4 KB | Display | |
Data in CIF | ![]() | 75.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wbxS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 5
NCS ensembles :
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Components
#1: Protein | Mass: 32184.816 Da / Num. of mol.: 4 / Fragment: RESIDUES 25-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11678.388 Da / Num. of mol.: 4 / Fragment: RESIDUES 22-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1044.117 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 3-AMINO-3-(2-NITRO)PHENYL-PROPIONIC ACID AT P7 / Source: (synth.) ![]() #4: Water | ChemComp-HOH / | Nonpolymer details | 3-AMINO-3-(2-NITRO)PHENYL-PROPIONIC ACID (PRQ): PHOTOCLEAV | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE AND 0.1 M CACODYLATE AT PH 6.4. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→20 Å / Num. obs: 50561 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WBX Resolution: 2.65→19.66 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.873 / SU B: 34.083 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→19.66 Å
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Refine LS restraints |
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