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Yorodumi- PDB-8uq8: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uq8 | |||||||||
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Title | Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker | |||||||||
Components | E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E | |||||||||
Keywords | TRANSFERASE / RNF168 / UbcH5c / Histone H2A / Histone H2B / Chromatin / Ubiquitin ligase / Ubiquitin-conjugating enzyme / DNA damage response / DNA double-strand break repair / PROTEIN BINDING / PROTEIN BINDING-Transferase complex | |||||||||
Function / homology | Function and homology information histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / positive regulation of protein targeting to mitochondrion ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / negative regulation of transcription elongation by RNA polymerase II / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / negative regulation of BMP signaling pathway / nucleosome binding / protein K48-linked ubiquitination / protein autoubiquitination / protein localization to CENP-A containing chromatin / SUMOylation of DNA damage response and repair proteins / Replacement of protamines by nucleosomes in the male pronucleus / interstrand cross-link repair / CENP-A containing nucleosome / Packaging Of Telomere Ends / ubiquitin ligase complex / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / 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 / positive regulation of DNA repair / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / TICAM1, RIP1-mediated IKK complex recruitment / DNA methylation / IKK complex recruitment mediated by RIP1 / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / ubiquitin binding / Defective pyroptosis / Negative regulators of DDX58/IFIH1 signaling / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Peroxisomal protein import / Nonhomologous End-Joining (NHEJ) / Regulation of TNFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein modification process / RING-type E3 ubiquitin transferase / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / G2/M DNA damage checkpoint / Inactivation of CSF3 (G-CSF) signaling / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / double-strand break repair via nonhomologous end joining / HCMV Early Events / Transcriptional regulation of granulopoiesis / protein polyubiquitination / structural constituent of chromatin / ubiquitin-protein transferase activity / UCH proteinases / ubiquitin protein ligase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / double-strand break repair / Antigen processing: Ubiquitination & Proteasome degradation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / site of double-strand break / HATs acetylate histones / antibacterial humoral response / Processing of DNA double-strand break ends / histone binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | |||||||||
Authors | Hu, Q. / Botuyan, M.V. / Mer, G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mol Cell / Year: 2024 Title: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Authors: Qi Hu / Debiao Zhao / Gaofeng Cui / Janarjan Bhandari / James R Thompson / Maria Victoria Botuyan / Georges Mer / Abstract: RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for ...RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uq8.cif.gz | 333.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uq8.ent.gz | 271.6 KB | Display | PDB format |
PDBx/mmJSON format | 8uq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/8uq8 ftp://data.pdbj.org/pub/pdb/validation_reports/uq/8uq8 | HTTPS FTP |
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-Related structure data
Related structure data | 8smwC 8smxC 8smyC 8smzC 8sn0C 8sn1C 8sn2C 8sn3C 8sn4C 8sn5C 8sn6C 8sn7C 8sn8C 8sn9C 8snaC 8txvC 8txwC 8txxC 8u13C 8u14C 8upfC 8uq9C 8uqaC 8uqbC 8uqcC 8uqdC 8uqeC 4gb0S 5eggS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules Aa
#1: Protein | Mass: 48807.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: residues 1-94 of RNF168, followed by residues 2-147 of UbcH5c, followed by residues 33-123 of H2B, followed by residues 12-105 of H2A Source: (gene. exp.) Homo sapiens (human) Gene: RNF168, UBE2D3, UBC5C, UBCH5C, H2BC21, H2BFQ, HIST2H2BE, H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE Production host: Escherichia coli (E. coli) References: UniProt: Q8IYW5, UniProt: P61077, UniProt: Q16778, UniProt: P04908, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme |
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-Non-polymers , 5 types, 227 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.89 Å3/Da / Density % sol: 68.41 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M ...Details: Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→50 Å / Num. obs: 61785 / % possible obs: 99.47 % / Redundancy: 7.6 % / Biso Wilson estimate: 34.28 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1093 / Rpim(I) all: 0.04232 / Rrim(I) all: 0.1172 / Net I/σ(I): 21.25 |
Reflection shell | Resolution: 2.34→2.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.8489 / Mean I/σ(I) obs: 4.42 / Num. unique obs: 6078 / CC1/2: 0.895 / CC star: 0.972 / Rpim(I) all: 0.3139 / Rrim(I) all: 0.8489 / % possible all: 98.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GB0, 5EGG Resolution: 2.34→36.06 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→36.06 Å
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Refine LS restraints |
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LS refinement shell |
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