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Yorodumi- PDB-4u1l: HLA class I micropolymorphisms determine peptide-HLA landscape an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u1l | |||||||||
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Title | HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin / HLA / HIV | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / activation of transmembrane receptor protein tyrosine kinase activity / host cell Golgi membrane / TAP binding ...symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / activation of transmembrane receptor protein tyrosine kinase activity / host cell Golgi membrane / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / 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 / endocytosis involved in viral entry into host cell / 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 / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / SH3 domain binding / virion component / 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 / 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 / MHC class II protein complex binding / early endosome membrane / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / 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 / virus-mediated perturbation of host defense response / Neutrophil degranulation / GTP binding / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / cell surface / Golgi apparatus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å | |||||||||
Model details | HLA-B8101 carrying RM9 peptide | |||||||||
Authors | Rizkallah, P.J. / Cole, D.K. / Fuller, A. / Sewell, A.K. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Retrovirology / Year: 2015 Title: A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape. Authors: Klverpris, H.N. / Cole, D.K. / Fuller, A. / Carlson, J. / Beck, K. / Schauenburg, A.J. / Rizkallah, P.J. / Buus, S. / Sewell, A.K. / Goulder, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u1l.cif.gz | 264.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u1l.ent.gz | 211.8 KB | Display | PDB format |
PDBx/mmJSON format | 4u1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u1l_validation.pdf.gz | 502.9 KB | Display | wwPDB validaton report |
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Full document | 4u1l_full_validation.pdf.gz | 520.7 KB | Display | |
Data in XML | 4u1l_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 4u1l_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/4u1l ftp://data.pdbj.org/pub/pdb/validation_reports/u1/4u1l | HTTPS FTP |
-Related structure data
Related structure data | 4u1hC 4u1iC 4u1jC 4u1kC 4u1mC 4u1nC 4u1sC 4i4wS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _
NCS ensembles :
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Details | Chains A, B and C form one biological entity. A second copy in the a.u. is formed by chains D, E and F |
-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 32058.270 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: Q31610, UniProt: P01889*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 1095.360 Da / Num. of mol.: 2 / Fragment: UNP residues 69-77 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q90VG9, UniProt: P03407*PLUS |
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-Non-polymers , 4 types, 349 molecules
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: 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: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M TRIS pH 8.0, 15% PEG 4000 and 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2012 / Details: mirrors | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.06→53.8 Å / Num. obs: 56594 / % possible obs: 97.7 % / Redundancy: 2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.092 / Net I/σ(I): 5.8 / Num. measured all: 112351 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 42.04 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I4W Resolution: 2.06→53.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2186 / WRfactor Rwork: 0.1781 / FOM work R set: 0.8439 / SU B: 6.193 / SU ML: 0.133 / SU R Cruickshank DPI: 0.1849 / SU Rfree: 0.1569 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.53 Å2 / Biso mean: 48.678 Å2 / Biso min: 8.3 Å2
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Refinement step | Cycle: final / Resolution: 2.06→53.8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.06→2.113 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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