Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking

2026-05-27 REL PDBc INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.title _citation.year _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.title _citation.year _citation_author.identifier_ORCID _em_admin.last_update PDBj PDBc 2025-05-16 2026-05-06 2026-05-06 2026-05-27 National Natural Science Foundation of China (NSFC) 22377059 China Not funded 2023YFA0913800 China Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Zhou CZ Li HT Shan XJ Ji GY Histone, Nucleosome, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex Shan X Ji G Li J Ren M Ma J Zhou Y Li H Zhou C DNA-histone cross-link locks the nucleosome structure and disrupts its recognition and processing. Protein Cell CN 17 476 482 2026 41206067 doi:10.1093/procel/pwaf094 1674-8018 9uz7 FULLOVERLAP EMDB EMD-64640 associated EM volume

Human canonical histone and 601 DNA Human canonical histone and 601 DNA 0 1 2 3 4 5 6 7 0.3 Human canonical histone with mutantion C96S/C110S/K115C 1 1 2 3 4 5 Homo sapiens 601 DNA with an alkynyl-dU modification at position 74 and a Cy5 fluorophore 1 6 7 Histone H3.1 2 1

H3 mutant, H3-C96S/C110S/K115C, in which Cys96 and Cys110 were substituted with Ser, leaving Cys115 as the sole reactive thiol

Homo sapiens Histone H3.1 2 2

H3 mutant, H3-C96S/C110S/K115C, in which Cys96 and Cys110 were substituted with Ser, leaving Cys115 as the sole reactive thiol that is crosslinked

Homo sapiens Histone H4 2 3

Recombinantly expressed human histone H4

Homo sapiens Histone H2A type 1-B/E 2 4

Recombinantly expressed human histone H2A.2

Homo sapiens Histone H2B type 1-J 2 5

Recombinantly expressed human histone H2B.1

Homo sapiens Histone H3.1 Homo sapiens 0.015247800999999998 1 Escherichia coli LEVO ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT DLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHACRVTIMPKDIQLARRIRGERA P68431 Histone H3.1 Homo sapiens 0.015304852 1 Escherichia coli LEVO ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT DLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHA(YCM)RVTIMPKDIQLARRIRGERA P68431 Histone H4 Homo sapiens 0.011263230999999999 2 Escherichia coli LEVO SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGFGG P62805 Histone H2A type 1-B/E Homo sapiens 0.014034354999999998 2 Escherichia coli LEVO SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK P04908 Histone H2B type 1-J Homo sapiens 0.013804045 2 Escherichia coli LEVO PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRL AHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P06899 DNA (145-MER) synthetic construct 0.045007660000000005 1 (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)(DG)(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) DNA DNA (145-MER) synthetic construct 0.044505370999999995 1 (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)(DC)(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) DNA singleParticle particle 0.18 7.6 10.0 C8H18N2O4S HESPS

10 mM HEPES, pH 7.6

Quantifoil R1.2/1.3 GOLD 300 PLASMA CLEANING 25 AIR

PDC-32G Plasma Cleaner

ETHANE 100 281 FEI VITROBOT MARK IV

cross-linked nucleosome via CuAAC method

TFS KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 64000.0 GATAN K3 (6k x 4k) 50.0 GATAN K3 (6k x 4k) 1978 50.0 1 1081772 NONE 8JBX 3.24 FSC 0.143 CUT-OFF cryoSPARC 199160 OTHER OTHER 2 NONE 8JBX 3.24 FSC 0.143 CUT-OFF 199160 emd_64640.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 216.00002 216.00002 216.00002 90.0 90.0 90.0 X Y Z -4.7296667 8.130012000000001 0.021586617 0.23679727 1.08 1.08 1.08 0.4 AUTHOR ::::EMDATABANK.org::::EMD-64640:::: 8JBX PDB experimental model

experimental model

RIGID BODY FIT REAL emd_64640_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 216.00002 216.00002 216.00002 90.0 90.0 90.0 X Y Z -0.6371092 2.223492 0.010936038 0.11972391 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-64640:::: emd_64640_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 216.00002 216.00002 216.00002 90.0 90.0 90.0 X Y Z -0.6489876 2.3934274 0.010886135 0.119588956 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-64640::::