2024-11-13 REL RCSB RCSB RCSB 2016-07-11 2016-07-27 2016-07-27 2024-11-13 Canadian Institutes of Health Research (CIHR) FDN143343 Canada Canadian Institutes of Health Research (CIHR) MOP81294 Canada Canadian Institutes of Health Research (CIHR) FDN143277 Canada Benlekbir S Wilson MD Sicheri F Rubinstein JL Durocher D DNA, chromatin, 53BP1, STRUCTURAL PROTEIN-DNA complex Wilson MD Benlekbir S Fradet-Turcotte A Sherker A Julien JP McEwan A Noordermeer SM Sicheri F Rubinstein JL Durocher D Nature UK 536 100 103 2016 27462807 doi:10.1038/nature18951 1476-4687 0006 NATUAS EMD-8247 other EM volume 5kgf FULLOVERLAP NCP-ubme/GST-53BP1 complex NCP-ubme/GST-53BP1 complex 0 1 2 3 4 5 6 7 8 9

Single-particle electrocryomicroscopy structure of Tandem Tudor domain and UDR region of human 53BP1 bound to a recombinant ubiquitylated and methylated nucleosome core particle

0.318 NCP-ubme 1 1 2 3 4 5 6 9

Modified nucleosome core particle, H2A enzymatically ubiquitylated on H2A K15, H4 chemically alkylated at K20C to create dimethyl lysine analog

unclassified 0.226 Widom-601 DNA 2 5 6

145 bp fragment of Widom-601 strong nuclesome positioning sequence, gift from Curt Davey (Vasudevan et. al, 2010, J.Mol.Biol.)

synthetic construct 0.88231 GST-53BP1 1 7 8

53BP1 Tandem Tudor domain and ubiquitin dependent recruitment region, artificially dimerized with Gluthaione-S-transferase (GST, not visible in structure)

Homo sapiens 0.0892 Ubiquitylated methylated histone octamer 2 1 2 3 4 9 unclassified 0.138 Histone H4kc20Me2 5 2

Dimethylated at position 20

Xenopus laevis Histone H3 5 1 Xenopus laevis Histone H2B.1 5 4 Homo sapiens Histone H2A.1 K13RK36R 5 3

Crosslinked at H2AK15 to ubiquitin at ub G76 (isopeptide bond)

Homo sapiens Ubiquitin 5 9

Crosslinked to H2A K15 (isopeptide bond)

Homo sapiens Histone H3.2 Xenopus laevis 0.015421101 2 Escherichia coli LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P84233 Histone H4 Xenopus laevis 0.011439511

cysteine alkylation at position 20

2 Escherichia coli LEVO MSGRGKGGKGLGKGGAKRHR(M2L)VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH AKRKTVTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A type 1 Homo sapiens 0.014163539

Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin

2 Escherichia coli LEVO MSGRGKQGGKARARAKSRSSRAGLQFPVGRVHRLLRRGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII PRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK P0C0S8 Histone H2B type 1-C/E/F/G/I Homo sapiens 0.013937212999999999 2 Escherichia coli LEVO MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASR LAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK P62807 DNA (145-MER) synthetic construct 0.044520383 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)(DG)(DA)(DT) DNA DNA (145-MER) synthetic construct 0.04499166 1 (DA)(DT)(DC)(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 Tumor suppressor p53-binding protein 1 Homo sapiens 0.0023767569999999997

full protein not modeled

2 Escherichia coli LEVO LTKAADISLDNLVEGKRKRRS H7BZY0 Ubiquitin Homo sapiens 0.008576831 2 Escherichia coli LEVO MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG P0CG47 singleParticle particle 0.6 7.5 10.0 C4H11NO3 Tris 30.0 KCl potassium chloride 0.5 EDTA 1.0 DTT

High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.

electron micrsocopy sciences COPPER/RHODIUM 400 CARBON HOLEY 20.0 GLOW DISCHARGE 10 AIR 0.039 ETHANE-PROPANE 100 277 FEI VITROBOT MARK III

Plunged into liquid ethane-propane (FEI VITROBOT MARK III).

FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 30.0 2.0 25000.0 34483.0 GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1-30 2 319 0.5 36.0 1 174185

Automatically picked from roughly 3000 particles using a manually picked template

1KX5

Resized to the same pixel size as the data and low-pass filtered to 40 Angstrom resolution

9 C2 FOURIER SPACE 4.54 FSC 0.143 CUT-OFF RELION 1.3 45361 PROJECTION MATCHING RELION 1.3 PROJECTION MATCHING RELION 1.3 10 RELION 1.3 RIGID BODY FIT

The atomic models of Widom-601 DNA (PDB ID 3LZ0), octameric histones (PDB ID 1KX5), ubiquitin (PDB ID 1UBI), and H4K20me2/53BP1 tandem Tudor domain (PDB ID 2IG0) were fitted without allowing flexibility into the 3D maps using UCSF Chimera. Segmentation was performed in UCSF Chimera. For the NCP-ubme structure the ubiquitin segmentation was further modified to remove obvious NCP density from the ubiquitin segment. The H2A/H2B sequence was mutated to the human H2AK13R/K36R and H2B manually in UCSF Chimera. A polyalanine model of the UDR was built within the UDR density in Coot, which compared well to predicted structures generated by Rosetta. The UDR model was mutated and fitted using UCSF Chimera, followed by iterative rounds of real-space refinement in PHENIX and model optimization in Coot. All figures were prepared in UCSF Chimera.

REAL 207.5