Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Mechanisms of RNF168 nucleosome recognition and ubiquitylation.
Journal, issue, pages	Mol Cell, Vol. 84, Issue 5, Page 839-853.e12, Year 2024
Publish date	Mar 7, 2024
Authors	Qi Hu / Debiao Zhao / Gaofeng Cui / Janarjan Bhandari / James R Thompson / Maria Victoria Botuyan / Georges Mer /
PubMed 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.
External links	Mol Cell / PubMed:38242129 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.049 - 4.0 Å
Structure data	40604 8smw EMDB-40604, PDB-8smw: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Method: EM (single particle) / Resolution: 3.3 Å 40605 8smx EMDB-40605, PDB-8smx: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Method: EM (single particle) / Resolution: 3.2 Å 40606 8smy EMDB-40606, PDB-8smy: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Method: EM (single particle) / Resolution: 3.2 Å 40607 8smz EMDB-40607, PDB-8smz: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Method: EM (single particle) / Resolution: 3.2 Å 40608 8sn0 EMDB-40608, PDB-8sn0: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Method: EM (single particle) / Resolution: 3.2 Å 40609 8sn1 EMDB-40609, PDB-8sn1: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Method: EM (single particle) / Resolution: 3.3 Å 40610 8sn2 EMDB-40610, PDB-8sn2: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Method: EM (single particle) / Resolution: 3.6 Å 40611 8sn3 EMDB-40611, PDB-8sn3: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Method: EM (single particle) / Resolution: 3.8 Å 40612 8sn4 EMDB-40612, PDB-8sn4: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Method: EM (single particle) / Resolution: 3.7 Å 40613 8sn5 EMDB-40613, PDB-8sn5: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Method: EM (single particle) / Resolution: 3.9 Å 40614 8sn6 EMDB-40614, PDB-8sn6: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Method: EM (single particle) / Resolution: 3.7 Å 40615 8sn7 EMDB-40615, PDB-8sn7: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Method: EM (single particle) / Resolution: 3.7 Å 40616 8sn8 EMDB-40616, PDB-8sn8: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Method: EM (single particle) / Resolution: 3.7 Å 40617 8sn9 EMDB-40617, PDB-8sn9: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Method: EM (single particle) / Resolution: 3.9 Å 40618 8sna EMDB-40618, PDB-8sna: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Method: EM (single particle) / Resolution: 4.0 Å 41706 8txv EMDB-41706, PDB-8txv: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Method: EM (single particle) / Resolution: 3.8 Å 41707 8txw EMDB-41707, PDB-8txw: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Method: EM (single particle) / Resolution: 3.6 Å 41708 8txx EMDB-41708, PDB-8txx: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Method: EM (single particle) / Resolution: 3.7 Å 41800 8u13 EMDB-41800, PDB-8u13: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Method: EM (single particle) / Resolution: 3.8 Å 41801 8u14 EMDB-41801, PDB-8u14: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Method: EM (single particle) / Resolution: 3.9 Å 42446 8upf EMDB-42446, PDB-8upf: Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Method: EM (single particle) / Resolution: 3.2 Å PDB-8uq8: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Method: X-RAY DIFFRACTION / Resolution: 2.34 Å PDB-8uq9: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-8uqa: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Method: X-RAY DIFFRACTION / Resolution: 2.049 Å PDB-8uqb: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Method: X-RAY DIFFRACTION / Resolution: 2.484 Å PDB-8uqc: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Method: X-RAY DIFFRACTION / Resolution: 2.61 Å PDB-8uqd: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Method: X-RAY DIFFRACTION / Resolution: 3.893 Å PDB-8uqe: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Method: X-RAY DIFFRACTION / Resolution: 3.562 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-CL: Unknown entry / Chloride ChemComp-GOL: GLYCEROL / Glycerol ChemComp-NA: Unknown entry ChemComp-HOH: WATER / Water
Source	homo sapiens (human)
Keywords	STRUCTURAL PROTEIN/DNA/TRANSFERASE / Nucleosome core particle / chromatin / RNF168 / RING domain / UbcH5c / DNA repair / DNA double-strand break / Homologous recombination / 53BP1 / ubiquitin / STRUCTURAL PROTEIN-DNA-TRANSFERASE complex / TRANSFERASE/DNA / TRANSFERASE / TRANSFERASE-DNA complex / MIU2-LRM domains / BRCA1-BARD1 / Histone H2A / Histone H2B / Ubiquitin ligase / Ubiquitin-conjugating enzyme / DNA damage response / DNA double-strand break repair / PROTEIN BINDING / PROTEIN BINDING-Transferase complex