2024-05-22 REL PDBe PDBe PDBe 2019-12-10 2019-12-18 2019-12-18 2024-05-22 Wellcome Trust United Kingdom Lancey C Hamdan SM Protein, REPLICATION Lancey C Tehseen M Raducanu VS Rashid F Merino N Ragan TJ Savva CG Zaher MS Shirbini A Blanco FJ Hamdan SM De Biasio A Nat Commun UK 11 1109 1109 2020 32111820 doi:10.1038/s41467-020-14898-6 2041-1723 EMD-10080 other EM volume EMD-10081 other EM volume EMD-10082 other EM volume 6tnz FULLOVERLAP Toolbelt Toolbelt 0 1 2 3 4 5 6 8 DNA polymerase 1 1 2 3 4 Homo sapiens Proliferating cell nuclear antigen, flap endonuclease 1 5 6 Homo sapiens DNA primer, template 1 7 8 synthetic construct DNA polymerase delta catalytic subunit Homo sapiens 0.123785922 1 Spodoptera frugiperda LEVO MDGKRRPGPGPGVPPKRARGGLWDDDDAPRPSQFEEDLALMEEMEAEHRLQEQEEEELQSVLEGVADGQVPPSAIDPRWL RPTPPALDPQTEPLIFQQLEIDHYVGPAQPVPGGPPPSRGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGFGPEH MGDLQRELNLAISRDSRGGRELTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRVAGLGTPS FAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKEKATQCQLEADVLWSDVVSHPPEGPWQRIAPLRVLSFDIECA GRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQN FDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVSFH FLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRGQQVKVVSQLL RQAMHEGLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRT PTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSV TGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFP YLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQ LVITKELTRAASDYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQ QLAKPLLRIFEPILGEGRAEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLSHQGAVCEFCQPRESELYQKE VSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQEQLLRRFGPPGPEAW P28340 2.7.7.7 DNA polymerase delta subunit 2 Homo sapiens 0.051338167999999997 1 Spodoptera frugiperda LEVO MFSEQAAQRAHTLLSPPSANNATFARVPVATYTNSSQPFRLGERSFSRQYAHIYATRLIQMRPFLENRAQQHWGSGVGVK KLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLA VFGSVRDDGKFLVEDYCFADLAPQKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSR VILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLAT AYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPH VYFCGNTPSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPISFSGFGAEDDDLGGLGLGP P49005 DNA polymerase delta subunit 3 Homo sapiens 0.0525285 1 Spodoptera frugiperda LEVO MWSHPQFEKADQLYLENIDEFVTDQNKIVTYKWLSYTLGVHVNQAKQMLYDYVERKRKENSGAQLHVTYLVSGSLIQNGH SCHKVAVVREDKLEAVKSKLAVTASIHVYSIQKAMLKDSGPLFNTDYDILKSNLQNCSKFSAIQCAAAVPRAPAESSSSS KKFEQSHLHMSSETQANNELTTNGHGPPASKQVSQQPKGIMGMFASKAAAKTQETNKETKTEAKEVTNASAAGNKAPGKG NMMSNFFGKAAMNKFKVNLDSEQAVKEEKIVEQPTVSVTEPKLATPAGLKKSSKKAEPVKVLQKEKKRGKRVALSDDETK ETENMRKKRRRIKLPESDSSEDEVFPDSPGAYEAESPSPPPPPSPPLEPVPKTEPEPPSVKSSSGENKRKRKRVLKSKTY LDGEGCIVTEKVYESESCTDSEEELNMKTSSVHRPPAMTVKKEPREERKGPKKGTAALGKANRQVSITGFFQRK Q15054 DNA polymerase delta subunit 4 Homo sapiens 0.016274323 1 Spodoptera frugiperda LEVO MHHHHHHSRAWRHPQFGGHHHHHHENLYFQSGRKRLITDSYPVVKRREGPAGHSKGELAPELGEEPQPRDEEEAELELLR QFDLAWQYGPCTGITRLQRWCRAKQMGLEPPPEVWQVLKTHPGDPRFQCSLWHLYPL Q9HCU8 Proliferating cell nuclear antigen Homo sapiens 0.029088061000000002 3 Escherichia coli BL21(DE3) LEVO GPHMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSK ILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDA VVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVV EYKIADMGHLKYYLAPKIEDEEGS P12004 Flap endonuclease 1 Homo sapiens 0.042617038999999995 1 Escherichia coli BL21(DE3) LEVO MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIK PVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAE ASCAALVKAGKVYAAATEDMACLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRG IGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEER IRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKRKEPEPKGSTKKKAKTGAAGKFKRGK P39748 3.1.-.- DNA primer synthetic construct 0.007665987 1 (DA)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DC)(DA)(DT)(DG)(DA)(DT)(DT)(DA)(DC)(DG)(DA) (DA)(DT)(DT)(DG)(DOC) DNA DNA template synthetic construct 0.011677539 1 (DC)(DT)(DG)(DC)(DA)(DC)(DG)(DA)(DA)(DT)(DT)(DA)(DA)(DG)(DC)(DA)(DA)(DT)(DT)(DC) (DG)(DT)(DA)(DA)(DT)(DC)(DA)(DT)(DG)(DG)(DT)(DC)(DA)(DT)(DA)(DG)(DC)(DT) DNA ZINC ION 6.5409e-05 1 ZN IRON/SULFUR CLUSTER 0.00035163999999999996 1 SF4 THYMIDINE-5'-TRIPHOSPHATE 0.000482168 1 TTP singleParticle particle 7.5 25.0 C8H18N2O4S HEPES 100.0 CH3CO2K Potassium Acetate 10.0 CaCl2 Calcium Chloride 0.02 H(C2H4O)nO(C6H4)C9H19 NP-40 0.4 C10H16N2O3S Biotin 1.0 C4H10O2S2 Dithiothreitol Quantifoil, UltrAuFoil, R1.2/1.3 GOLD 300 GRAPHENE OXIDE CONTINUOUS GLOW DISCHARGE 300 ETHANE 100 277 FEI VITROBOT MARK IV

Complex separated by gel filtration

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.1 2.3000000000000003 105000.0 57471.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 77.0 OTHER GATAN K3 BIOQUANTUM (6k x 4k) 11520 8184 1 5071 3.0 44.0

Data were collected in super resolution mode

1

Relion initial model

C1 4.05 FSC 0.143 CUT-OFF RELION 3.1 47291 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION 3.1 8