2024-07-24 REL PDBe PDBe PDBe 2023-04-05 2023-07-26 2023-07-26 2024-07-24 EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND 847543 Germany European Research Council (ERC) 833613 European Union German Research Foundation (DFG) CRC136 Germany German Research Foundation (DFG) CRC1064 Germany CryoEM Structure INO80core Hexasome complex Arp5 Ies6 refinement state1 Zhang M Jungblut A Hoffmann T Eustermann S ATP-dependent chromatin remodeler, DNA BINDING PROTEIN Zhang M Jungblut A Kunert F Hauptmann L Hoffmann T Kolesnikova O Metzner F Moldt M Weis F DiMaio F Hopfner KP Eustermann S Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling. Science US 381 313 319 2023 37384673 doi:10.1126/science.adf6287 1095-9203 0038 SCIEAS Afonine PV Poon BK Read RJ Sobolev OV Terwilliger TC Urzhumtsev A Adams PD Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol 74 531 544 2018 29872004 doi:10.1107/S2059798318006551 2059-7983 Emsley P Lohkamp B Scott WG Cowtan K Features and development of Coot. Acta Crystallogr D Biol Crystallogr US 66 486 501 2010 20383002 doi:10.1107/S0907444910007493 1399-0047 ABCRE6 EMD-17006 other EM volume
composite map
 EMD-17010 other EM volume
Focused map / local refinement
 EMD-17019 other EM volume
Consensus map
 8oof FULLOVERLAP INO80 core module in complex with hexasome INO80 core module in complex with hexasome 0 1 2
11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct INO80 + hexasome has an overall weight of 1.1MDa Ino80, Ies2, Ies6, Ies4,Arp6, Rvb1, Rvb2, Arp8, Arp4, Actin, Taf14 Hexasome DNA, 2xH3, 2xH4, H2A, H2B
Thermochaetoides thermophila 0.861 Chromatin-remodeling complex subunit IES6 Thermochaetoides thermophila 0.023127523 1 Trichoplusia ni LEVO MSNPDAQSAQAAHQALVEQLDLHSIHKTFRNPNWRPNQRRNKTIKAILGESQRKEASSTSAVATPRADDNGGGSGADTPA NNDNNDGLSTSGTSTPANGNGSGAGTPASNGQPNLAQASRSLQKLVLEKSLASAQAPDKKAANGFASSAPTATYTNIESA PSLAPMKHYCDVTGLPAPYLDPKTRLRYHNKEIFAMIRNLPQGMGEQFLEARGAHTVLK G0S590 Actin-related protein 5 Thermochaetoides thermophila 0.08777308599999999 1 Trichoplusia ni LEVO MAPSAVAEPPPIPQRDEPWKRLPPPTVYPVKEARFEKYIPPQLDGRERALAQPPGQVAIVIDNGSHSVRAGWNFEDKPRL AIPPIMSKYRDRKMGKTFSFAGSDCYADTTARSHIRNAFEAGTGIVSNWDVMEHVLDYVFVKLGMNECDGAIDMPIVMTE AVANLPYSRKSMSEIIFECYGAPSLVYGIDSLFSFRHNQGQTGLVVSSSYSATHVIPVYNRKALLSQAIRLNWGGWHMAE YMLKLLKLKYYTGFPGKLNSSQTEHMVRDFCYVSLDYDRELAGYLDWTGLEDRERIVQYPYTEEVVVQKTEEELARIAER KKESGRRLQEQAAKMRLERLMKKEQELEYYKDIQRRMQGESKKEIKRLLDEAELKDEAALERVIRDLERSIKRARQKDLG EPEEEEVPDFSLLDVPDDQLDEAGLRQKRQQRLLKSNWEARQRAKAEKEAEKARLAEEARLDEERRKNDLEGWLEEKRQL RLAKLNQLKERERLKADLGNRKSLASQIRMKNIANLASDNPTGSGSRKRRRGGAGADQDDDFGADDADWGVYRSVAIGAN KGDDSDDEEGEEDLEAAIRSLENDLLRYDKTFSYDMTLDAQRDWSKSLLHAFRYGPRPFDPSSQAETHRVHLNVERIRVP EVLFQPAAIAGVDQAGLVEIAGDILCQRLPSLPGIQDAPDAFLRDVFLTGGNTLFQNFDERLRQGLMALLPVGAPLRVRR AQDAILDAWRGAAGWACTEEAKAAWITREEYLEKGGEYIKEHDLGNAFA G0S589 ADENOSINE-5'-TRIPHOSPHATE 0.000507181 1 ATP MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 0.88 7.5
30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
 Quantifoil R2/1 COPPER 200 CARBON HOLEY PLASMA CLEANING
10% oxygene 90% argon
 ETHANE 100 281 FEI VITROBOT MARK IV
wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807).
11-subunit ctINO80 reconstituted with hexasome
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 15384 50.36 1 2137460
Particles were initially picked by WARP to generate an initial model, which was subsequently used for the 3D template picking
 2.9 FSC 0.143 CUT-OFF RELION 1.4 72400 MAXIMUM LIKELIHOOD RELION 4.0
de novo 3D model was generated by using gradient-driven algorithm implemented in RELION 4.0
 MAXIMUM LIKELIHOOD emd_17012.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.92 295.92 295.92 90.0 90.0 90.0 X Y Z -0.37033167 1.7242944 0.00060694723 0.013470144 0.822 0.822 0.822 0.144 AUTHOR ctINO80-hexasome complex Arp5 Ies6 focused refinement sharpened map 6FML PDB experimental model OTHER emd_17012_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.92 295.92 295.92 90.0 90.0 90.0 X Y Z -0.008749579 0.033503074 0.00009814149 0.00094877393 0.822 0.822 0.822 AUTHOR ctINO80-hexasome complex Arp5 Ies6 focused refinement unsharpened map emd_17012_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.92 295.92 295.92 90.0 90.0 90.0 X Y Z -0.028592655 0.040770408 0.00009926014 0.001779141 0.822 0.822 0.822 AUTHOR ctINO80-hexasome complex Arp5 Ies6 focused refinement half map 2 emd_17012_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.92 295.92 295.92 90.0 90.0 90.0 X Y Z -0.026331363 0.040253516 0.00009706859 0.0017922104 0.822 0.822 0.822 AUTHOR ctINO80-hexasome complex Arp5 Ies6 focused refinement half map 1