2024-04-03 REL PDBe PDBe PDBe 2022-09-07 2023-09-20 2023-09-20 2024-04-03 European Research Council (ERC) European Union Knut and Alice Wallenberg Foundation Sweden Swedish Research Council Sweden Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome Bacic L Gaullier G Deindl S ALC1, CHD1L, nucleosome, PARylation, ADP-ribosylation, post-translational modification, chromatin, DNA BINDING PROTEIN Bacic L Gaullier G Mohapatra J Mao G Brackmann K Panfilov M Liszczak G Sabantsev A Deindl S Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1. Nat Commun UK 15 1000 1000 2024 38307862 doi:10.1038/s41467-024-45237-8 2041-1723 EMD-13065 other EM volume
Previous study
 EMD-13070 other EM volume
Previous study
 8b0a FULLOVERLAP Complex between ALC1 and a site-specifically PARylated nucleosome Complex between ALC1 and a site-specifically PARylated nucleosome 0 1 2 3 4 5 6 7
Site-specific ADP-ribosylation was introduced as described in https://doi.org/10.7554/elife.71502
Homo sapiens 0.30457 Chromodomain-helicase-DNA-binding protein 1-like Homo sapiens 0.098906766 1 Escherichia coli LEVO MFLLRLHTEGRAEAARVQEQDLRQWGLTGIHLRSYQLEGVNWLAQRFHCQNGCILGDEMGLGKTCQTIALFIYLAGRLND EGPFLILCPLSVLSNWKEEMQRFAPGLSCVTYAGDKEERACLQQDLKQESRFHVLLTTYEICLKDASFLKSFPWSVLVVD EAHRLKNQSSLLHKTLSEFSVVFSLLLTGTPIQNSLQELYSLLSFVEPDLFSKEEVGDFIQRYQDIEKESESASELHKLL QPFLLRRVKAEVATELPKKTEVVIYHGMSALQKKYYKAILMKDLDAFENETAKKVKLQNILSQLRKCVDHPYLFDGVEPE PFEVGDHLTEASGKLHLLDKLLAFLYSGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQQPI FVFLLSTRAGGVGMNLTAADTVIFVDSDFNPQNDLQAAARAHRIGQNKSVKVIRLIGRDTVEEIVYRKAASKLQLTNMII EGGHFTLGAQKPAADADLQLSEILKFGLDKLLASEGSTMDEIDLESILGETKDGQWVSDALPAAEGGSRDQEEGKNHMYL FEGKDYSKEPSKEDRKSFEQLVNLQKTLLEKASQEGRSLRNKGSVLIPGLVEGSTKRKRVLSPEELEDRQKKRQEAAAKR RRLIEEKKRQKEEAEHKKKMAWWESNNYQSFCLPSEESEPEDLENGEESSAELDYQDPDATSLKYVSGDVTHPQAGAEDA LIVHCVDDSGHWGRGGLFTALEKRSAEPRKIYELAGKMKDLSLGGVLLFPVDDKESRNKGQDLLALIVAQHRDRSNVLSG IKMAALEEGLKKIFLAAKKKKASVHLPRIGHATKGFNWYGTERLIRKHLAARGIPTYIYYFPRSKAHHHHHH Q86WJ1 3.6.4.12 Histone H3 Xenopus laevis 0.015403061999999999 2 Escherichia coli LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA A0A310TTQ1 Histone H4 Xenopus laevis 0.011394426 2 Escherichia coli LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A type 1 Xenopus laevis 0.014109436 2 Escherichia coli LEVO MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII PRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK P06897 Histone H2B 1.1 Xenopus laevis 0.013655948 2 Escherichia coli LEVO MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAH YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P02281 DNA (149-MER) Widom 601 sequence synthetic construct 0.049175336 1 (DT)(DC)(DT)(DA)(DG)(DG)(DT)(DG)(DA)(DC)(DC)(DA)(DT)(DC)(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)(DG)(DA)(DT)(DA)(DG)(DG)(DC) DNA DNA (149-MER) Widom 601 sequence synthetic construct 0.049606586 1 (DG)(DC)(DC)(DT)(DA)(DT)(DC)(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)(DG)(DA)(DT)(DG)(DG)(DT)(DC)(DA)(DC)(DC)(DT)(DA)(DG)(DA) DNA singleParticle particle 7.5 Quantifoil R2/2 COPPER 200 GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 2 22155 37.6 1 Ab initio model from RELION InitialModel job. 3.0 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 212256 MAXIMUM LIKELIHOOD RELION 3.1.3 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1
Non-uniform refinement in cryoSPARC
 cryoSPARC 3.3.1
Split of 3DVA results in cryoSPARC.
 emd_15777.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 220.5952 220.5952 220.5952 90.0 90.0 90.0 X Y Z -0.12974726 0.39591178 0.0033953001 0.021941448 0.8617 0.8617 0.8617 0.08 AUTHOR Map from non-uniform refinement of 212 256 particles in cryoSPARC. 7OTQ PDB experimental model FLEXIBLE FIT REAL emd_15777_msk_2.map emd_15777_msk_1.map emd_15777_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 220.5952 220.5952 220.5952 90.0 90.0 90.0 X Y Z -0.03686143 1.9653426 0.0034122805 0.041887034 0.8617 0.8617 0.8617 AUTHOR Main map denoised with deepEMhancer, using the "highRes" denoising model. emd_15777_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 220.5952 220.5952 220.5952 90.0 90.0 90.0 X Y Z -0.194764 0.46003583 0.0019696534 0.028934903 0.8617 0.8617 0.8617 AUTHOR Half-map B from non-uniform refinement in cryoSPARC. emd_15777_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 220.5952 220.5952 220.5952 90.0 90.0 90.0 X Y Z -0.20253606 0.50524765 0.0019931474 0.028980568 0.8617 0.8617 0.8617 AUTHOR Half-map A from non-uniform refinement in cryoSPARC.