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Yorodumi- PDB-1h15: X-ray crystal structure of HLA-DRA1*0101/DRB5*0101 complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h15 | |||||||||
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Title | X-ray crystal structure of HLA-DRA1*0101/DRB5*0101 complexed with a peptide from Epstein Barr Virus DNA polymerase | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/TRANSFERASE / COMPLEX (MHC-ANTIGEN) / IMMUNE SYSTEM / MHC / HLA / CLASS II / DR2 / DRB5 / EBV / DNA POLYMERASE / DNA-DIRECTED DNA POLYMERASE / IMMUNE SYSTEM-TRANSFERASE complex | |||||||||
Function / homology | Function and homology information : / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / bidirectional double-stranded viral DNA replication ...: / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / bidirectional double-stranded viral DNA replication / positive regulation of memory T cell differentiation / exonuclease activity / transport vesicle membrane / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / type II interferon-mediated signaling pathway / MHC class II antigen presentation / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / DNA replication / adaptive immune response / lysosome / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / immune response / lysosomal membrane / Golgi membrane / nucleotide binding / host cell nucleus / cell surface / DNA binding / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Lang, H. / Jacobsen, H. / Ikemizu, S. / Andersson, C. / Harlos, K. / Madsen, L. / Hjorth, P. / Sondergaard, L. / Svejgaard, A. / Wucherpfennig, K. ...Lang, H. / Jacobsen, H. / Ikemizu, S. / Andersson, C. / Harlos, K. / Madsen, L. / Hjorth, P. / Sondergaard, L. / Svejgaard, A. / Wucherpfennig, K. / Stuart, D.I. / Bell, J.I. / Jones, E.Y. / Fugger, L. | |||||||||
Citation | Journal: Nat.Immunol. / Year: 2002 Title: A Functional and Structural Basis for Tcr Cross-Reactivity in Multiple Sclerosis Authors: Lang, H. / Jacobsen, H. / Ikemizu, S. / Andersson, C. / Harlos, K. / Madsen, L. / Hjorth, P. / Sondergaard, L. / Svejgaard, A. / Wucherpfennig, K. / Stuart, D.I. / Bell, J.I. / Jones, E.Y. / Fugger, 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h15.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h15.ent.gz | 136.4 KB | Display | PDB format |
PDBx/mmJSON format | 1h15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/1h15 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/1h15 | HTTPS FTP |
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-Related structure data
Related structure data | 1fv1S 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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2 |
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Unit cell |
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-Components
-HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 21155.904 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN, RESIDUES 26-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P01903 #2: Protein | Mass: 22231.574 Da / Num. of mol.: 2 / Fragment: BETA CHAIN, RESIDUES 30-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q30126, UniProt: Q30154*PLUS |
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-Protein/peptide / Non-polymers , 2 types, 32 molecules CF
#3: Protein/peptide | Mass: 1628.850 Da / Num. of mol.: 2 / Fragment: RESIDUES 628-641 / Source method: obtained synthetically Details: THE PROTEIN OCCURS NATURALLY IN EBV BUT THE PEPTIDE WAS SYNTHESISED CHEMICALLY Source: (synth.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) / References: UniProt: P03198, DNA-directed DNA polymerase #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 4 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Details
Sequence details | RESIDUES 26-207 OF DATABASE SEQUENCE RESIDUES 30-219 OF DATABASE SEQUENCE |
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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: 2.54 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.5 Details: 14% PEG 3550, 100MM GLYCINE AND 10MM TRIS AT PH 3.5-4.0. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9686 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI111 / SI311 CRYSTALS, LN2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 28750 / % possible obs: 94.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.414 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.1→3.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.1 / % possible all: 78.9 |
Reflection | *PLUS Num. measured all: 166287 |
Reflection shell | *PLUS % possible obs: 78.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SINGLE COPY OF 1FV1 (A AND B CHAINS) MINUS PEPTIDE Resolution: 3.1→19.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 64350.38 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.1 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 3.3 Å |