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Open data
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Basic information
| Entry | Database: PDB / ID: 9tnz | ||||||||||||||||||||||||
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| Title | SP100 CARD filament | ||||||||||||||||||||||||
Components | Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100 | ||||||||||||||||||||||||
Keywords | IMMUNE SYSTEM / Innate immunity / interferon / DNA damage / cryo-EM | ||||||||||||||||||||||||
| Function / homology | Function and homology informationregulation of Fas signaling pathway / regulation of viral process / maintenance of protein location / chromo shadow domain binding / response to type I interferon / negative regulation of protein export from nucleus / negative regulation of viral transcription / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway ...regulation of Fas signaling pathway / regulation of viral process / maintenance of protein location / chromo shadow domain binding / response to type I interferon / negative regulation of protein export from nucleus / negative regulation of viral transcription / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / detection of maltose stimulus / maltose transport complex / carbohydrate transport / regulation of angiogenesis / carbohydrate transmembrane transporter activity / response to retinoic acid / type II interferon-mediated signaling pathway / maltose binding / maltose transport / response to type II interferon / maltodextrin transmembrane transport / SUMOylation of DNA damage response and repair proteins / retinoic acid receptor signaling pathway / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to cytokine / nuclear periphery / ATP-binding cassette (ABC) transporter complex / telomere maintenance / cell chemotaxis / DNA damage response, signal transduction by p53 class mediator / PML body / kinase binding / Interferon gamma signaling / transcription corepressor activity / outer membrane-bounded periplasmic space / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / periplasmic space / chromosome, telomeric region / protein dimerization activity / nuclear body / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
| Biological species | ![]() Homo sapiens (human) | ||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.52 Å | ||||||||||||||||||||||||
Authors | Rabl, J. / Aird, E. / Corn, J. | ||||||||||||||||||||||||
| Funding support | European Union, Switzerland, 3items
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Citation | Journal: Nat Cell Biol / Year: 2026Title: An SP110-SP100 axis is a critical regulator of promyelocytic leukaemia body dynamics and mitotic fidelity. Authors: Eric J Aird / Julius Rabl / Tabea Knuesel / Kevin Groen / Samah W Awwad / Boris Korablev / Lynn Scherpe / Waleed Al-Herz / Robin Hupfer / Mike Recher / Stephen P Jackson / Benjamin G Hale / Jacob E Corn / ![]() Abstract: Stimulation of the innate immune system by foreign RNA elicits a potent interferon response and can trigger cell death. The mechanisms by which cells balance a robust response with cell-intrinsic ...Stimulation of the innate immune system by foreign RNA elicits a potent interferon response and can trigger cell death. The mechanisms by which cells balance a robust response with cell-intrinsic lethality are still being uncovered. Here, using genome-wide CRISPR-Cas9 genetic screens with triphosphorylated RNA stimulation, we discover that promyelocytic leukaemia (PML) nuclear body-localized speckled protein 110 (SP110) is a potent inhibitor of type 1 interferon-driven cell death. Death suppression by SP110 counteracts a toxic activity of SP100, a major constituent of PML bodies. Loss of SP110 leads to mitotic retention of SP100 and PML bodies, which associate with and perturb segregating chromosomes, leading to micronucleus formation, DNA damage and genotoxic cell death. A combination of cryo-electron microscopy, AlphaFold modelling and cellular biochemistry reveals that SP110 dissolves toxic SP100 oligomers via necessary and sufficient direct interactions between their caspase activation and recruitment domains. These data reveal the critical roles of SP100 and SP110 in governing the disassembly of PML bodies during mitosis, as well as the repercussions if this process is misregulated. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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| PDBx/mmCIF format | 9tnz.cif.gz | 701.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9tnz.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9tnz.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/9tnz ftp://data.pdbj.org/pub/pdb/validation_reports/tn/9tnz | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 56096MC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Assembly
| Deposited unit | ![]()
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| Noncrystallographic symmetry (NCS) | NCS domain:
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Homo sapiens (human)
Switzerland, 3items
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