2024-05-29 REL RCSB RCSB RCSB 2020-10-02 2021-09-15 2021-09-15 2024-05-29 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM132111 United States Japan Society for the Promotion of Science (JSPS) JSPS Overseas Research Fellowships Japan Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Arimura Y Funabiki H nucleosome, interphase, cell cycle, chromatin, DNA BINDING PROTEIN, STRUCTURAL PROTEIN-DNA complex Arimura Y Shih RM Froom R Funabiki H Structural features of nucleosomes in interphase and metaphase chromosomes. Mol.Cell US 81 4377 2021 34478647 doi:10.1016/j.molcel.2021.08.010 1097-2765 2168 MOCEFL 7kbd FULLOVERLAP Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) 0 1 2 3 4 5 6 Xenopus laevis Histone H3.2 Xenopus laevis 0.015421101 2 LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P84233 Histone H4 Xenopus laevis 0.011394426 2 LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A Xenopus laevis 0.014883174 2 LEVO MSGRGKKVQKAASGKASRSAKAGLQFPVGRIHRLLRKGNYAVRIGSGSAIYLAATLEYLCAEVLELAGNAARDNKKLRIM PRHIQLAVRNDDELAKLFEGVTIADGGVLPNIQSALLPKKTVKGSSSSQEPTAVESQEF Q6DKE3 Histone H2B 1.1 Xenopus laevis 0.013965265 2 LEVO MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASR LAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P02281 DNA (151-MER) Xenopus laevis 0.046847863 1 (DA)(DG)(DG)(DA)(DT)(DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(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)(DG)(DT)(DG)(DA)(DT)(DA) DNA DNA (151-MER) Xenopus laevis 0.046355543 1 (DT)(DA)(DT)(DC)(DA)(DC)(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)(DG)(DA)(DT) (DT)(DG)(DT)(DG)(DA)(DT)(DA)(DT)(DC)(DC)(DT) DNA singleParticle particle 7.4 10.0 HEPES-KOH 30.0 KCl KCl 1.0 EGTA EGTA 0.3 Leupeptin 0.3 Pepstatin 0.3 Chymostatin 1.0 Sodium Butyrate 1.0 beta-glycerophosphate 1.0 trehalose 0.1 1,6,-hexanediol Quantifoil R1.2/1.3 GOLD 300 GLOW DISCHARGE OTHER
20W
 ETHANE 100 277 FEI VITROBOT MARK IV FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 33.11 1 C1 3.38 FSC 0.143 CUT-OFF RELION 3 89191 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION RELION 3 emd_22790.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 294.0 294.0 294.0 90.0 90.0 90.0 X Y Z -0.14137341 0.27648535 0.0000043825844 0.008476911 1.47 1.47 1.47 0.043 AUTHOR Fliped and rescaled map for atomic model creation 6DZT PDB experimental model 5NL0 PDB experimental model emd_22790_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.31216103 1.166944 0.0020922087 0.05603708 1.5 1.5 1.5 AUTHOR 3D classification map for structural variation analysis emd_22790_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.33323005 1.2831628 0.0013188733 0.06493239 1.5 1.5 1.5 AUTHOR 3D classification map for structural variation analysis emd_22790_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.38428208 1.299927 0.0013945578 0.0610834 1.5 1.5 1.5 AUTHOR 3D classification map for structural variation analysis emd_22790_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.45403674 1.3901736 0.0005205266 0.06368507 1.5 1.5 1.5 AUTHOR 3D classification map for structural variation analysis emd_22790_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.47114292 1.3086557 0.0010219053 0.062620066 1.5 1.5 1.5 AUTHOR 3D classification map for structural variation analysis emd_22790_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.343977 1.2431636 0.0023226321 0.0570002 1.5 1.5 1.5 AUTHOR 3D classification map for structural variation analysis emd_22790_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.31362334 1.283686 0.0016996945 0.06285802 1.5 1.5 1.5 AUTHOR 3D classification map for structural variation analysis emd_22790_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.4209159 1.1601855 0.0029322868 0.05960954 1.5 1.5 1.5 AUTHOR 3D classification map for structural variation analysis emd_22790_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.04822424 0.1108646 0.0000033819754 0.004129259 1.5 1.5 1.5 AUTHOR Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) emd_22790_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.04396011 0.11125087 0.0000053831936 0.0041346387 1.5 1.5 1.5 AUTHOR Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)