+Open data
-Basic information
Entry | Database: PDB / ID: 4o2c | ||||||
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Title | An Nt-acetylated peptide complexed with HLA-B*3901 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig-like | ||||||
Function / homology | Function and homology information positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of chemokine (C-C motif) ligand 5 production / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / RNA secondary structure unwinding ...positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of chemokine (C-C motif) ligand 5 production / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / RNA secondary structure unwinding / gamete generation / NLRP3 inflammasome complex / positive regulation of protein K63-linked ubiquitination / cellular response to arsenic-containing substance / poly(A) binding / P granule / RNA stem-loop binding / cellular response to osmotic stress / gamma-tubulin binding / regulation of interleukin-12 production / regulation of dendritic cell differentiation / negative regulation of non-canonical NF-kappaB signal transduction / regulation of T cell anergy / regulation of interleukin-6 production / positive regulation of NLRP3 inflammasome complex assembly / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / ribosomal small subunit binding / positive regulation of translational initiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / transcription factor binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / negative regulation of intrinsic apoptotic signaling pathway / signaling adaptor activity / stress granule assembly / translation initiation factor binding / TAP binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / translational initiation / positive regulation of protein autophosphorylation / protection from natural killer cell mediated cytotoxicity / 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 / DNA helicase activity / detection of bacterium / positive regulation of interferon-beta production / protein serine/threonine kinase activator activity / ribonucleoside triphosphate phosphatase activity / intrinsic apoptotic signaling pathway / secretory granule membrane / cytosolic ribosome assembly / positive regulation of translation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / chromosome segregation / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to virus / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / mRNA 5'-UTR binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / positive regulation of protein serine/threonine kinase activity / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / negative regulation of cell growth / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / Wnt signaling pathway / positive regulation of T cell cytokine production / cellular response to virus / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cytoplasmic stress granule / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Authors | Sun, M. / Liu, J. / Qi, J. / Tefsen, B. / Shi, Y. / Yan, J. / Gao, G.F. | ||||||
Citation | Journal: J.Immunol. / Year: 2014 Title: N alpha-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted n alpha-acetylpeptide presentation Authors: Sun, M. / Liu, J. / Qi, J. / Tefsen, B. / Shi, Y. / Yan, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o2c.cif.gz | 186.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o2c.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 4o2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/4o2c ftp://data.pdbj.org/pub/pdb/validation_reports/o2/4o2c | HTTPS FTP |
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-Related structure data
Related structure data | 4o2eC 4o2fC 2bstS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 31714.873 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P30475, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 966.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00571 |
#4: 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: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 17% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2010 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 41844 / Num. obs: 41844 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.72 Å2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BST Resolution: 1.802→30.559 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8914 / SU ML: 0.16 / σ(F): 0.1 / Phase error: 17.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.197 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.59 Å2 / Biso mean: 18.7783 Å2 / Biso min: 1.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.802→30.559 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: 12.3268 Å / Origin y: 9.0104 Å / Origin z: 18.62 Å
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Refinement TLS group | Selection details: ALL |