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Yorodumi- PDB-1d5m: X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDE AND SEB -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d5m | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDE AND SEB | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PEPTIDE INHIBITOR / MHC CLASS II-SUPERANTIGEN COMPLEX / IMMUNE SYSTEM-PEPTIDE INHIBITOR COMPLEX / PEPTIDOMIMETIC INHIBITOR | ||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Staphylococcus aureus (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Swain, A.L. / Crowther, R. / Kammlott, U. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2000 Title: Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures. Authors: Bolin, D.R. / Swain, A.L. / Sarabu, R. / Berthel, S.J. / Gillespie, P. / Huby, N.J. / Makofske, R. / Orzechowski, L. / Perrotta, A. / Toth, K. / Cooper, J.P. / Jiang, N. / Falcioni, F. / ...Authors: Bolin, D.R. / Swain, A.L. / Sarabu, R. / Berthel, S.J. / Gillespie, P. / Huby, N.J. / Makofske, R. / Orzechowski, L. / Perrotta, A. / Toth, K. / Cooper, J.P. / Jiang, N. / Falcioni, F. / Campbell, R. / Cox, D. / Gaizband, D. / Belunis, C.J. / Vidovic, D. / Ito, K. / Crowther, R. / Kammlott, U. / Zhang, X. / Palermo, R. / Weber, D. / Guenot, J. / Nagy, Z. / Olson, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d5m.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d5m.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d5m_validation.pdf.gz | 470.6 KB | Display | wwPDB validaton report |
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Full document | 1d5m_full_validation.pdf.gz | 483.4 KB | Display | |
Data in XML | 1d5m_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 1d5m_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d5m ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d5m | HTTPS FTP |
-Related structure data
Related structure data | 1d5xC 1d5zC 1d6eC 1sebS 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
-HLA CLASS II HISTOCOMPATIBILITY ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21084.826 Da / Num. of mol.: 1 / Fragment: DR ALPHA CHAIN, EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01903 |
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#2: Protein | Mass: 22505.994 Da / Num. of mol.: 1 / Fragment: DR-4 BETA CHAIN, EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P13760, UniProt: P01911*PLUS |
-Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 148 molecules CD
#3: Protein | Mass: 28411.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P01552 |
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#4: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 929.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: N-acetyl-3-cyclohexyl-L-alanyl-N~5~-[amino(iminio)methyl]-L-ornithyl-L-alanyl-L-methionyl-S-[(acetylamino)methyl]-L- cysteinyl-L-seryl-L-leucinamide |
#5: Sugar | ChemComp-NAG / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | INHIBITOR WAS BOUND TO MHC; SUBSEQUENT |
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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: 2.63 Å3/Da / Density % sol: 53.17 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 5% PEG 4000, 0.01 M NA ACETATE, PH 5, 2.4% ETHYLENE GLYCOL, pH 7.4 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9686 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 50025 / % possible obs: 94.5 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.078 |
Reflection shell | Highest resolution: 2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SEB Resolution: 2→19.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 429125.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.22 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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