2025-11-05 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-05-02 2025-11-05 2025-11-05 2025-11-05 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM132111 United States Cryo-EM analysis of human H2A.Z on methylated 601L DNA Shih RM Arimura Y Nucleosome, H2A.Z, DNA methylation, DNA BINDING PROTEIN Shih RM Arimura Y Konishi HA Funabiki H Impacts of DNA methylation on H2A.Z deposition and nucleosome stability To Be Published 0353 EMD-70480 other EM volume
Map of unmethylated 601L counterpart
 EMD-70474 other EM volume
H2A.Z nucleosome on Sat2R-P DNA
 EMD-70473 other EM volume
H2A.Z nucleosome on methylated Sat2R-P DNA
 9oh2 FULLOVERLAP EMDB EMD-70481 associated EM volume
Cryo-EM analysis of human H2A.Z on methylated 601L DNA
 EMDB EMD-70480 other EM volume
Map of unmethylated 601L counterpart
 EMDB EMD-70474 other EM volume
H2A.Z nucleosome on Sat2R-P DNA
 EMDB EMD-70473 other EM volume
H2A.Z nucleosome on methylated Sat2R-P DNA
 PDB 9OH1 unspecified
Unmethylated 601L counterpart
 PDB 9OGS unspecified
H2A.Z nucleosome on Sat2R-P DNA
 PDB 9OGZ unspecified
H2A.Z nucleosome on Sat2R-P DNA
 PDB 9OGR unspecified
H2A.Z nucleosome on methylated Sat2R-P DNA
 PDB 9OH0 unspecified
H2A.Z nucleosome on methylated Sat2R-P DNA
 Human H2A.Z nucleosome on methylated Sat2R-P DNA Human H2A.Z nucleosome on methylated Sat2R-P DNA 0 1 2 3 4 5 6 Homo sapiens 0.2 Histone H3.2 Homo sapiens 0.015421101 2 Escherichia coli BL21 LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA Q71DI3 Histone H4 Homo sapiens 0.011394426 2 Escherichia coli BL21 LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG P62805 Histone H2A.Z Homo sapiens 0.013450601 2 Escherichia coli BL21 LEVO AGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKR ITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGQQKTV P0C0S5 Histone H2B type 1-J Homo sapiens 0.013935238999999999 2 Escherichia coli BL21 LEVO MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASR LAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P06899 601L DNA (137-MER) synthetic construct 0.044985961 1 (DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(5CM)(DG)(DG)(DT)(DG)(DC)(5CM)(DG)(DA) (DG)(DG)(DC)(5CM)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(5CM)(DG)(DT)(DA) (DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(5CM)(DG)(DC)(DT)(DT) (DA)(DA)(DA)(5CM)(DG)(DC)(DA)(5CM)(DG)(DT)(DA)(5CM)(DG)(DG)(DA)(DA)(DT)(DC)(5CM) (DG)(DT)(DA)(5CM)(DG)(DT)(DG)(5CM)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(5CM)(DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(5CM)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG)(DA)(DG)(5CM)(DG)(DG)(DC)(DC)(DT)(5CM)(DG)(DG)(DC)(DA)(DC) (5CM)(DG)(DG)(DG)(DA)(DT)(DT)(DG)(DT)(DG)(DA)(DT) DNA 601L DNA (137-MER) synthetic construct 0.044976945 1 (DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(5CM)(DG)(DG)(DT)(DG)(DC)(5CM)(DG)(DA) (DG)(DG)(DC)(5CM)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(5CM)(DG)(DT)(DA) (DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(5CM)(DG)(DC)(DT)(DT) (DA)(DA)(DA)(5CM)(DG)(DC)(DA)(5CM)(DG)(DT)(DA)(5CM)(DG)(DG)(DA)(DT)(DT)(DC)(5CM) (DG)(DT)(DA)(5CM)(DG)(DT)(DG)(5CM)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(5CM)(DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(5CM)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG)(DA)(DG)(5CM)(DG)(DG)(DC)(DC)(DT)(5CM)(DG)(DG)(DC)(DA)(DC) (5CM)(DG)(DG)(DG)(DA)(DT)(DT)(DG)(DT)(DG)(DA)(DT) DNA singleParticle particle 7.5 Quantifoil R1.2/1.3 GOLD 400 GRAPHENE PLASMA CLEANING ETHANE 100 298 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 2.5 GATAN K3 (6k x 4k) 50.0 1 1542751 PHASE FLIPPING AND AMPLITUDE CORRECTION 3WA9
3WA9 was used as starting model for histone core. A modified version of 3UT9 was used to generate the starting model for DNA.
 3.14 FSC 0.143 CUT-OFF 179360 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_70481.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 330.24 330.24 330.24 90.0 90.0 90.0 X Y Z -1.560373 2.6840413 0.000109170214 0.058191977 0.85999995 0.85999995 0.85999995 0.18 AUTHOR RIGID BODY FIT emd_70481_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 330.24 330.24 330.24 90.0 90.0 90.0 X Y Z -2.17414 2.4089477 0.0003376587 0.2507015 0.85999995 0.85999995 0.85999995 AUTHOR emd_70481_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 330.24 330.24 330.24 90.0 90.0 90.0 X Y Z -2.3186545 2.0944316 0.00033617523 0.24943055 0.85999995 0.85999995 0.85999995 AUTHOR