2024-05-22 REL PDBe PDBe PDBe 2019-05-09 2019-09-25 2019-09-25 2024-05-22 The Francis Crick Institute FC0010061 United Kingdom The Francis Crick Institute FC0010065 United Kingdom Renault L Maskell DP Wilson MD Cherepanov P Costa A chromatin, nucleosome, retrovirus, DNA BINDING PROTEIN Wilson MD Renault L Maskell DP Ghoneim M Pye VE Nans A Rueda DS Cherepanov P Costa A Nat Commun UK 10 4189 4189 2019 31519882 doi:10.1038/s41467-019-12007-w 2041-1723 Wilson MD Renault L Maskell DP Ghoneim M Pye VE Nans A Rueda DS Cherepanov P Costa A Nat Commun UK 10 4189 4189 2019 31519882 doi:10.1038/s41467-019-12007-w 2041-1723 EMD-4692 other EM volume

D02 nucleosome in absence of PFV intasome

6rny FULLOVERLAP Nucleosome core particle bound by PFV intasome post in the post catalytic state Nucleosome core particle bound by PFV intasome post in the post catalytic state 0 1 2 3 4 5 6 7 8 9 10

human histones refolded as an octamer with native human D02 sequence. PFV intasome formed form short annealed oligos and PFV integrase. complex formed by mixing and separated by SEC. Catalysis initiated by addition of Magnesium ions

0.399 Nucleosome 1 1 2 3 4

Nucleosome

Homo sapiens Integrase 1 5

Integrase

Human spumaretrovirus Human DNA 1 6 7 8 9

Human DNA

Homo sapiens DNA 1 10

DNA

Pyrobaculum filamentous virus 1 Histone H3.3 Homo sapiens 0.015360983 2 Escherichia coli LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P84243 Histone H4 Homo sapiens 0.011394426 2 Escherichia coli LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG P62805 Histone H2A type 1 Homo sapiens 0.014121537 2 Escherichia coli LEVO MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII PRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK P0C0S8 Histone H2B type 1-C/E/F/G/I Homo sapiens 0.013937212999999999 2 Escherichia coli LEVO MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASR LAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK P62807 Integrase Human spumaretrovirus 0.044456695 4 Escherichia coli LEVO GPGCNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIA NLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYP TKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVG RPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPSTPPASSRSWSP VVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE P14350 2.7.7.49 DNA (128-MER) Homo sapiens 0.039189093999999994 1 (DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC)(DA)(DT)(DG)(DA)(DC)(DA)(DC)(DT)(DA)(DC) (DC)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DG)(DA)(DA)(DA)(DC)(DA)(DG)(DG)(DT)(DT)(DT)(DC) (DA)(DC)(DC)(DA)(DG)(DC)(DC)(DA)(DG)(DG)(DC)(DC)(DT)(DT)(DG)(DA)(DA)(DT)(DG)(DC) (DA)(DA)(DT)(DT)(DG)(DT)(DC)(DT)(DT)(DA)(DC)(DT)(DA)(DG)(DG)(DA)(DA)(DT)(DA)(DT) (DT)(DT)(DG)(DG)(DA)(DC)(DT)(DT)(DC)(DC)(DC)(DC)(DA)(DC)(DC)(DT)(DA)(DC)(DC)(DA) (DT)(DT)(DC)(DA)(DG)(DG)(DT)(DA)(DA)(DC)(DT)(DT)(DG)(DA)(DT)(DA)(DC)(DA)(DA)(DA) (DC)(DA)(DC)(DA)(DG)(DC)(DC)(DC) DNA DNA (108-MER) Homo sapiens 0.033581453 1 (DG)(DG)(DG)(DC)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG)(DT)(DA)(DT)(DC)(DA)(DA)(DG)(DT) (DT)(DA)(DC)(DC)(DT)(DG)(DA)(DA)(DT)(DG)(DG)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DG)(DG) (DA)(DA)(DG)(DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DT)(DT)(DC)(DC)(DT)(DA)(DG)(DT)(DA) (DA)(DG)(DA)(DC)(DA)(DA)(DT)(DT)(DG)(DC)(DA)(DT)(DT)(DC)(DA)(DA)(DG)(DG)(DC)(DC) (DT)(DG)(DG)(DC)(DT)(DG)(DG)(DT)(DG)(DA)(DA)(DA)(DC)(DC)(DT)(DG)(DT)(DT)(DT)(DC) (DC)(DT)(DG)(DG)(DG)(DA)(DA)(DG) DNA DNA (33-MER) Homo sapiens 0.010114522999999999 1 (DG)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DT)(DC)(DT)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DG)(DT) (DG)(DA)(DA)(DA)(DA)(DC)(DC)(DA)(DA)(DC)(DT)(DA)(DA) DNA DNA (53-MER) Homo sapiens 0.016397531 1 (DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC)(DA)(DT)(DG)(DA)(DC)(DA)(DG)(DT)(DA)(DG) (DT)(DT)(DA)(DG)(DT)(DT)(DG)(DG)(DT)(DT)(DT)(DT)(DC)(DA)(DC)(DC)(DA)(DC)(DA)(DG) (DG)(DG)(DA)(DG)(DA)(DA)(DC)(DC)(DT)(DG)(DG)(DA)(DC) DNA DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3') Pyrobaculum filamentous virus 1 0.005834794 2 (DA)(DT)(DT)(DG)(DT)(DC)(DA)(DT)(DG)(DG)(DA)(DA)(DT)(DT)(DT)(DC)(DG)(DC)(DA) DNA MAGNESIUM ION 2.4305e-05 2 MG singleParticle particle 0.1 7.0 1.0 DTT C-flat-1/1 COPPER 400 CARBON HOLEY PLASMA CLEANING ETHANE 80 277 LEICA EM CPC

1 min incubation 3.5s blot.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.0015 0.0035 59000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN Microscope was modified with a Cs corrector (NeCEN netherlands) FEI FALCON II (4k x 4k) INTEGRATING 2 4916 1.6 56.0 1 3125

initial model based EMDB-2992 low pass filtered to 50A

3 C1 FOURIER SPACE 3.9 FSC 0.143 CUT-OFF RELION 1.3 177155 MAXIMUM LIKELIHOOD RELION 1.3 MAXIMUM LIKELIHOOD RELION 1.3 4 59000.0 RELION 1.3

Two rounds of 3D classification. First with 8 classes coarse sampling, second with 4 classes.

3UTB PDB experimental model 3OS0 PDB experimental model

The initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.real_space_refine and namdinator. Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix.

REAL emd_4960_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.02433156 0.080862634 -0.000060545528 0.0046424423 1.12 1.12 1.12 AUTHOR ::::EMDATABANK.org::::EMD-4960:::: Half map 1 of Nucleosome core particle bound by PFV intasome post catalytic state emd_4960_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.024836516 0.08269778 -0.000060940114 0.004638865 1.12 1.12 1.12 AUTHOR ::::EMDATABANK.org::::EMD-4960:::: Half map 1 of Nucleosome core particle bound by PFV intasome post catalytic state