2024-10-16 REL PDBe PDBe PDBe 2019-06-13 2019-06-26 2019-12-18 2024-10-16 German Research Foundation SFB860, SPP1935 Germany European Research Council 693023 Germany Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Wang H Farnung L LEDGF, PWWP, H3K36me3, nucleosome, TRANSCRIPTION Wang H Farnung L Dienemann C Cramer P Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding. Nat.Struct.Mol.Biol. US 27 8 13 2020 31819277 doi:10.1038/s41594-019-0345-4 1545-9985 6s01 FULLOVERLAP H3K36me3 nucleosome-LEDGF complex H3K36me3 nucleosome-LEDGF complex 0 1 2 3 4 5 6 7
H3K36me3 introduced by methyl-lysine analog method, only the density of PWWP domain of LEDGF is visible in the structure
0.25 Histone proteins 1 1 2 3 4 Xenopus laevis PC4 and SFRS1-interacting protein 1 7 Homo sapiens Wisdom 601 DNA (165-MER) 1 5 6 synthetic construct Histone H3 Xenopus laevis 0.015331982
residue K36 was chemically modified to be ML3.
2 Escherichia coli LEVO ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGV(ML3)KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ DFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA A0A310TTQ1 Histone H4 Xenopus laevis 0.011263230999999999 2 Escherichia coli LEVO SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A Xenopus laevis 0.013978240999999999 2 Escherichia coli LEVO SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK Q6AZJ8 Histone H2B 1.1 Xenopus laevis 0.013524752 2 Escherichia coli LEVO AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHY NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P02281 Wisdom 601 DNA (165-MER) synthetic construct 0.050699315999999994 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)(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)(DT)(DA)(DC)(DA) (DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DC)(DA) (DG)(DC)(DG)(DA)(DC) DNA Wisdom 601 DNA (165-MER) synthetic construct 0.051170601999999996 1 (DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC)(DA) (DC)(DA)(DG)(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)(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) (DC)(DT)(DG)(DA)(DT) DNA PC4 and SFRS1-interacting protein Homo sapiens 0.060224453
density of residue 30-34 and residue 92-530 are invisible
1 Trichoplusia ni LEVO MTRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNKRKGFNEG LWEIDNNPKVKFSSQQAATKQSNASSDVEVEEKETSVSKEDTDHEEKASNEDVTKAVDITTPKAARRGRKRKAEKQVETE EAGVVTTATASVNLKVSPKRGRPAATEVKIPKPRGRPKMVKQPCPSESDIITEEDKSKKKGQEEKQPKKQPKKDEEGQKE EDKPRKEPDKKEGKKEVESKRKNLAKTGVTSTSDSEEEGDDQEGEKKRKGGRNFQTAHRRNMLKGQHEKEAADRKRKQEE QMETEQQNKDEGKKPEVKKVEKKRETSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTL KKIRRFKVSQVIMEKSTMLYNKFKNMFLVGEGDSVITQVLNKSLAEQRQHEEANKTKDQGKKGPNKKLEKEQTGSKTLNG GSDAQDGNQPQHNGESNEDSKDNHEASTKKKPSSEERETEISLKDSTLDN O75475 singleParticle particle 0.2 7.5 20.0 C8H18N2O4S HEPES 50.0 NaCl sodium chloride 1.0 C4H10O2S2 Dithiothreitol
Solution were made from stock solution
 Quantifoil, UltrAuFoil GOLD 200 GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV
blot for 4 seconds before plunging.
the complex is purified by gel filtration
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K2 SUMMIT (4k x 4k) COUNTING 9.0 43.18 1 527640 cryoSPARC ab-initio reconstruction was use to generate the startup model. 1 C1 3.2 FSC 0.143 CUT-OFF RELION 3.0.5 55142 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION RELION 3.0.5 emd_10069.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.13748676 0.27593878 0.0005588795 0.00729526 1.05 1.05 1.05 0.05 AUTHOR cryo-EM structure of LEDGF bound H3K36me3 modified nucleosome. 3MVD PDB experimental model RIGID BODY FIT Cross-correlation coefficient REAL 120.0 emd_10069_msk_1.map emd_10069_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.025969341 0.09605531 0.0007239511 0.0044842972 1.05 1.05 1.05 AUTHOR half map 1 emd_10069_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.027659286 0.096628726 0.0007293725 0.0044933185 1.05 1.05 1.05 AUTHOR half map 2