+Open data
-Basic information
Entry | Database: PDB / ID: 6biz | |||||||||
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Title | HLA-DRB1 in complex with citrullinated Histone 2B peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis | |||||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / 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 / Generation of second messenger molecules / negative regulation of type II interferon production / immunological synapse / PD-1 signaling / epidermis development / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / MHC class II antigen presentation / detection of bacterium / RNA Polymerase I Promoter Opening / T cell receptor binding / DNA methylation / Condensation of Prophase Chromosomes / trans-Golgi network membrane / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / HDACs deacetylate histones / lumenal side of endoplasmic reticulum membrane / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / protein tetramerization / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / clathrin-coated endocytic vesicle membrane / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / ER to Golgi transport vesicle membrane / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / structural constituent of cytoskeleton / cognition / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / MHC class II protein complex / Transcriptional regulation of granulopoiesis / 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 / nucleosome / Downstream TCR signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MHC class II protein complex binding / late endosome membrane / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / HATs acetylate histones / T cell receptor signaling pathway / Senescence-Associated Secretory Phenotype (SASP) / early endosome membrane / Oxidative Stress Induced Senescence / positive regulation of canonical NF-kappaB signal transduction / Estrogen-dependent gene expression / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Ting, Y.T. / Scally, S.W. / Rossjohn, J. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis. Authors: Ting, Y.T. / Petersen, J. / Ramarathinam, S.H. / Scally, S.W. / Loh, K.L. / Thomas, R. / Suri, A. / Baker, D.G. / Purcell, A.W. / Reid, H.H. / Rossjohn, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6biz.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6biz.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 6biz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/6biz ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6biz | HTTPS FTP |
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-Related structure data
Related structure data | 6bijC 6bilC 6binC 6birC 6bivC 6bixC 6biyC 4mdiS 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 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21919.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P01903 |
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#2: Protein | Mass: 23294.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q29890, UniProt: P01911*PLUS |
-Protein/peptide / Sugars , 2 types, 3 molecules C
#3: Protein/peptide | Mass: 1693.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8N257*PLUS |
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#4: Sugar |
-Non-polymers , 2 types, 223 molecules
#5: Chemical | ChemComp-B3P / |
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#6: 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: 2.73 Å3/Da / Density % sol: 54.88 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 22-28% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.09 Å / Num. obs: 31731 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 24.0655815872 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03453 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.05→2.18 Å / Rmerge(I) obs: 0.88 / CC1/2: 0.191 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MDI Resolution: 2.1→39.246 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39.246 Å
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Refine LS restraints |
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LS refinement shell |
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