+Open data
-Basic information
Entry | Database: PDB / ID: 8pp7 | ||||||
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Title | human RYBP-PRC1 bound to mononucleosome | ||||||
Components |
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Keywords | GENE REGULATION / ncPRC1 complex / nucleosome / H2A / histones / RING1B / BMI1 / heterodimer / E3 ligase / K119 | ||||||
Function / homology | Function and homology information regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression ...regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / RING-like zinc finger domain binding / Oxidative Stress Induced Senescence / PRC1 complex / sex chromatin / rostrocaudal neural tube patterning / segment specification / polytene chromosome / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex / positive regulation of immature T cell proliferation in thymus / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / negative regulation of gene expression, epigenetic / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / hemopoiesis / MLL1 complex / humoral immune response / negative regulation of apoptotic signaling pathway / heterochromatin / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / positive regulation of B cell proliferation / nucleosomal DNA binding / epigenetic regulation of gene expression / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / promoter-specific chromatin binding / apoptotic signaling pathway / brain development / RING-type E3 ubiquitin transferase / euchromatin / negative regulation of DNA-binding transcription factor activity / heterochromatin formation / structural constituent of chromatin / positive regulation of fibroblast proliferation / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / chromatin organization / mitotic cell cycle / chromosome / gene expression / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / nuclear body / protein ubiquitination / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Drosophila melanogaster (fruit fly) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å | ||||||
Authors | Ciapponi, M. / Benda, C. / Mueller, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1. Authors: Maria Ciapponi / Elena Karlukova / Sven Schkölziger / Christian Benda / Jürg Müller / Abstract: Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified ...Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pp7.cif.gz | 426.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pp7.ent.gz | 313.4 KB | Display | PDB format |
PDBx/mmJSON format | 8pp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pp7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8pp7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8pp7_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 8pp7_validation.cif.gz | 67 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/8pp7 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/8pp7 | HTTPS FTP |
-Related structure data
Related structure data | 17797MC 8pp6C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 6 types, 12 molecules KMLNAEBFCGDH
#1: Protein | Mass: 38152.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMI1, PCGF4, RNF51 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35226 #2: Protein | Mass: 38062.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF2, BAP1, DING, HIPI3, RING1B / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q99496, RING-type E3 ubiquitin transferase #3: Protein | Mass: 15289.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: H3_1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7L0PXJ3 #4: Protein | Mass: 11521.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His4r, BcDNA:RH52884, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, CG3379, Dmel_CG3379 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4KFZ9 #5: Protein | Mass: 13257.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865 Production host: Escherichia coli (E. coli) / References: UniProt: P84051 #6: Protein | Mass: 13727.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, ...Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910 Production host: Escherichia coli (E. coli) / References: UniProt: P02283 |
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-DNA chain , 2 types, 2 molecules JI
#7: DNA chain | Mass: 76716.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#8: DNA chain | Mass: 76481.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 1 types, 8 molecules
#9: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 58.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146136 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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