2024-01-17 REL RCSB RCSB RCSB 2021-11-21 2022-03-02 2022-03-02 2024-01-17 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01-GM084192 United States 2.7 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state. This entry contains a better resolved DNA-binding domain Nodelman IM Das S Faustino AM Fried SD Bowman GD Armache J-P CHD1, chromatin remodeling, ATPase, DBD, nucleosome, remodeling, transcription, DNA BINDING PROTEIN Nodelman IM Das S Faustino AM Fried SD Bowman GD Armache JP Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. Nat.Struct.Mol.Biol. US 29 121 129 2022 35173352 doi:10.1038/s41594-021-00719-x 1545-9985 EMD-25479 other EM volume EMD-25481 other EM volume EMD-25483 other EM volume EMD-25484 other EM volume Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state 0
This entry has a weak DNA-binding domain
Saccharomyces cerevisiae 0.4 singleParticle particle 1.7 7.0
20 mM HEPES, pH 7.0, 60 mM KCl, 1.5 mM DTT, 1 mM MgCl2
 Quantifoil R2/2 COPPER 200 CARBON HOLEY GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK IV
Nucleosome-bound CHD1, prepared in the presence of ATPgammaS, and then crosslinked using GraFix.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 -1.0 4.0 -2.2 28.0 81000.0 46296.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 (6k x 4k) 11520 8184 1 6906 3.3 49.9 1
Data collected in Super Resolution at 0.54A/pixel. Motion corrected, 1.5x fourier binned, dose-weighed
10900948 Ab initio model from cryoSPARC C1 BACK PROJECTION 2.7 FSC 0.143 CUT-OFF cryoSPARC 3.2 75867 PROJECTION MATCHING cryoSPARC 3.2 PROJECTION MATCHING cryoSPARC 3.2 emd_25480.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 311.04 311.04 311.04 90.0 90.0 90.0 X Y Z -0.60284597 2.2154746 0.0022696375 0.059299413 0.972 0.972 0.972 0.37 AUTHOR Sharpened 2.7A map with a negative bfactor (-17) in an orientation aligned to a common reference 3LZ0 PDB experimental model 3MWY A PDB experimental model OTHER
phenix.real_space_refine
REAL emd_25480_msk_1.map emd_25480_msk_2.map emd_25480_msk_3.map emd_25480_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 311.04 311.04 311.04 90.0 90.0 90.0 X Y Z 0.0 1.8665074 0.009528907 0.05055606 0.972 0.972 0.972 AUTHOR emd_25480_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 311.04 311.04 311.04 90.0 90.0 90.0 X Y Z 0.0 2.2141423 0.009528908 0.053488713 0.972 0.972 0.972 AUTHOR Unsharpened 2.7A map in an orientation aligned to a common reference. emd_25480_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 311.04 311.04 311.04 90.0 90.0 90.0 X Y Z -0.7708502 2.678589 0.0022696175 0.06536613 0.972 0.972 0.972 AUTHOR Sharpened 2.7A map with a negative bfactor (-17) unaligned to a common reference emd_25480_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 311.04 311.04 311.04 90.0 90.0 90.0 X Y Z -0.915197 2.5893185 0.0029426066 0.11590666 0.972 0.972 0.972 AUTHOR half-map 1 (half_A) from cryoSPARC emd_25480_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 311.04 311.04 311.04 90.0 90.0 90.0 X Y Z -0.84122306 2.6258206 0.0029840672 0.11656675 0.972 0.972 0.972 AUTHOR half-map 2 (half_B) from cryoSPARC