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- PDB-3mre: Crystal Structure of MHC class I HLA-A2 molecule complexed with E... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mre | ||||||
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Title | Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288 nonapeptide | ||||||
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![]() | IMMUNE SYSTEM / MHC class I / HLA / IMMUNE RESPONSE / NONAPEPTIDE / VIRAL PEPTIDE / EPSTEIN-BARR VIRUS / BMLF1 PROTEIN / EB2 protein | ||||||
Function / homology | ![]() symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / mRNA transport / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / cellular response to iron ion / 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 / specific granule lumen / recycling endosome membrane / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of type II interferon production / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / virus-mediated perturbation of host defense response / innate immune response / host cell nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gras, S. / Echasserieau, K. / Saulquin, X. / Bonneville, M. / Housset, D. | ||||||
![]() | ![]() Title: Analysis of Relationships between Peptide/MHC Structural Features and Naive T Cell Frequency in Humans. Authors: Reiser, J.B. / Legoux, F. / Gras, S. / Trudel, E. / Chouquet, A. / Leger, A. / Le Gorrec, M. / Machillot, P. / Bonneville, M. / Saulquin, X. / Housset, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121 KB | Display | ![]() |
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PDB format | ![]() | 92.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.1 KB | Display | ![]() |
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Full document | ![]() | 451.9 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mrcC ![]() 3mrdC ![]() 3mrgC ![]() 3mrhC ![]() 3mrlC ![]() 3mroC ![]() 3mrrC ![]() 3gsoS C: citing same article ( 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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Components
#1: Protein | Mass: 34008.711 Da / Num. of mol.: 1 / Fragment: HLA-A*0201 alpha chain, UNP resiude 25-300 / Mutation: A245V Source method: isolated from a genetically manipulated source Details: C-terminal biotin acceptor peptide sequence tag (GSLHHILDAQKMVWNHR) Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 920.191 Da / Num. of mol.: 1 Fragment: EB2 PROTEIN FRAGMENT (BMLF1 280-288), UNP residues 300-308 Source method: obtained synthetically / Details: chemical synthesis Source: (synth.) ![]() References: UniProt: Q3KSU1 |
#4: Water | ChemComp-HOH / |
Compound details | EBV BSFL2 AND BMLF1 ORFS ARE JOINED TO ENCODE THE EB2 PROTEIN. EB2 PROTEIN IS ALSO CALLED ...EBV BSFL2 AND BMLF1 ORFS ARE JOINED TO ENCODE THE EB2 PROTEIN. EB2 PROTEIN IS ALSO CALLED BSFL2/BMLF1, MTA OR SM. |
Sequence details | THE GLCTLVAML NONAPEPTIDE WAS FIRST IDENTIFIED AS AN HLA-A2 RESTRICTED T CELL EPITOPE ON A ...THE GLCTLVAML NONAPEPTID |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 6000, 0.1M NaCitrate, 0.1M NaCl, 5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 16, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→50 Å / Num. obs: 150866 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 12.358 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GSO Resolution: 1.1→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.551 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. ...Details: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. Rwork and Rfree values corresponds to the coordinates just before these very last cycles.
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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 max: 53.59 Å2 / Biso mean: 12.51 Å2 / Biso min: 2.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.128 Å / Total num. of bins used: 20
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