Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)

2025-06-25 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name PDBj PDBj 2023-11-24 2024-08-07 2024-08-07 2025-06-25 National Natural Science Foundation of China (NSFC) 22137005, 92253302, 22227810 for L. Liu, and 22277073 for M. Pan China Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Ai HS Tong ZB Deng ZH Pan M Liu L RNF168, nucleosome, H2AK13/15 ubiquitination, NUCLEAR PROTEIN, NUCLEAR PROTEIN-DNA complex Ai H Tong Z Deng Z Shi Q Tao S Liang J Sun M Wu X Zheng Q Liang L Li JB Gao S Tian C Liu L Pan M Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168 Biorxiv US 2024 doi:10.1101/2024.01.02.573964 2692-8205 8x7k FULLOVERLAP cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) 0 1 2 3 4 5 6 7 8 9 Homo sapiens Histone H3.2 Homo sapiens 0.011401267999999999 2 Escherichia coli LEVO PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRV TIMPKDIQLARRIRGER Q71DI3 Histone H4 Homo sapiens 0.009352003 2 Escherichia coli LEVO KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG FG P62805 Histone H2A type 1-B/E Homo sapiens 0.011482382 1 Escherichia coli LEVO ACTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEEL NKLLGRVTIAQGGVLPNIQAVLLPK P04908 Histone H2B type 1-K Homo sapiens 0.010477994000000001 2 Escherichia coli LEVO RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHA VSEGTKAVTKYTSA O60814 Histone H2A type 1-B/E Homo sapiens 0.011807769 1 Escherichia coli LEVO ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN DEELNKLLGRVTIAQGGVLPNIQAVLLP P04908 DNA (143-MER) Homo sapiens 0.04435924199999999 1 (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC) DNA DNA (143-MER) Homo sapiens 0.04391897299999999 1 (DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA) (DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG) (DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA) (DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC) (DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC) (DC)(DT)(DG) DNA Ubiquitin-conjugating enzyme E2 D3 Homo sapiens 0.016657937999999997 1 Escherichia coli LEVO MALKRINKELSDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS NGSICLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM P61077 2.3.2.23 E3 ubiquitin-protein ligase RNF168 Homo sapiens 0.012987123 1 Escherichia coli LEVO MALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYHTRRNSLVNVELWTII QKHYPRECKLRASGQESEEVADDYQPVRLLSKP Q8IYW5 2.3.2.27 ZINC ION 6.5409e-05 2 ZN singleParticle particle 7.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 GATAN K3 (6k x 4k) 50.0 1 NONE 3.27 FSC 0.143 CUT-OFF 147576 RANDOM ASSIGNMENT ANGULAR RECONSTITUTION emd_38101.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 274.944 274.944 274.944 90.0 90.0 90.0 X Y Z -0.022449065 0.06863741 0.00021433667 0.0019520313 1.074 1.074 1.074 0.01 AUTHOR ::::EMDATABANK.org::::EMD-38101:::: emd_38101_msk_1.map emd_38101_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 274.944 274.944 274.944 90.0 90.0 90.0 X Y Z -0.009215001 0.03341231 0.00022215667 0.0016265418 1.074 1.074 1.074 AUTHOR ::::EMDATABANK.org::::EMD-38101:::: Cryo-EM map of RNF168/UbcH5c-Ub/monoubiquitinated nucleosome complex at a resolution of 6.2 angstrom emd_38101_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 274.944 274.944 274.944 90.0 90.0 90.0 X Y Z -0.02242339 0.0608112 0.00005133315 0.002274265 1.074 1.074 1.074 AUTHOR ::::EMDATABANK.org::::EMD-38101:::: emd_38101_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 274.944 274.944 274.944 90.0 90.0 90.0 X Y Z -0.022582995 0.06257196 0.000029131532 0.002269745 1.074 1.074 1.074 AUTHOR ::::EMDATABANK.org::::EMD-38101::::