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Yorodumi- PDB-2v2w: T CELL CROSS-REACTIVITY AND CONFORMATIONAL CHANGES DURING TCR ENG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2w | |||||||||
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Title | T CELL CROSS-REACTIVITY AND CONFORMATIONAL CHANGES DURING TCR ENGAGEMENT | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / COMPLEX (ANTIGEN-PEPTIDE) / TCR / HIV / MHC / AIDS / MHC I / HLA-A2 / MEMBRANE / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / UBL CONJUGATION / IMMUNE RESPONSE / DISEASE MUTATION / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE | |||||||||
Function / homology | Function and homology information 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 ...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 / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of receptor-mediated endocytosis / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / endoplasmic reticulum membrane / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / Golgi apparatus / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) HUMAN IMMUNODEFICIENCY VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Lee, J.K. / Stewart-Jones, G. / Dong, T. / Harlos, K. / Di Gleria, K. / Dorrell, L. / Douek, D.C. / Van Der Merwe, P.A. / Jones, E.Y. / Mcmichael, A.J. | |||||||||
Citation | Journal: J.Exp.Med. / Year: 2004 Title: T Cell Cross-Reactivity and Conformational Changes During Tcr Engagement. Authors: Lee, J.K. / Stewart-Jones, G. / Dong, T. / Harlos, K. / Di Gleria, K. / Dorrell, L. / Douek, D.C. / Van Der Merwe, P.A. / Jones, E.Y. / Mcmichael, A.J. | |||||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v2w.cif.gz | 196 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2w.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v2w_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 2v2w_full_validation.pdf.gz | 468.8 KB | Display | |
Data in XML | 2v2w_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 2v2w_validation.cif.gz | 67.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2w ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2w | HTTPS FTP |
-Related structure data
Related structure data | 2v2xC 1hhiS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 2 / Fragment: PEPTIDE BINDING DOMAIN, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769 #3: Protein/peptide | Mass: 981.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS #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: 2.19 Å3/Da / Density % sol: 51.83 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 101204 / % possible obs: 86.5 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.76 / % possible all: 41.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHI Resolution: 1.6→72.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.033 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.113 / 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: 23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→72.55 Å
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Refine LS restraints |
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