Cryo-EM structure of the DNA-bound PolD-PCNA processive complex from P. abyssi

2025-12-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation citation_author _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_PubMed _citation.title STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _pdbx_entry_details.has_protein_modification DATA_COLLECTION em_admin _em_admin.last_update PDBe PDBe 2019-10-24 2020-03-04 2020-03-04 2025-12-17 French National Research Agency ANR-17-CE11-0005-01 France Knut and Alice Wallenberg Foundation KAW 2015.0234 Sweden Swedish Research Council 2017-04641 Sweden Cryo-EM structure of the DNA-bound PolD-PCNA processive complex from P. abyssi Madru C Raia P PCNA, DP2, PolD, DP1, REPLICATION, PIP-box Madru C Henneke G Raia P Hugonneau-Beaufet I Pehau-Arnaudet G England P Lindahl E Delarue M Carroni M Sauguet L Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Nat Commun UK 11 1591 1591 2020 32221299 doi:10.1038/s41467-020-15392-9 2041-1723 6t8h FULLOVERLAP EMDB EMD-10401 associated EM volume

DNA-bound PolD-PCNA processive complex from P. abyssi DNA-bound PolD-PCNA processive complex from P. abyssi 0 1 4 5 310 PolD-PCNA processive complex 1 1 2 3 Pyrococcus abyssi DNA 1 4 5 synthetic construct DNA polymerase sliding clamp Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.029471763999999998 3 Escherichia coli LEVO MRGSHHHHHHGSMPFEIVFEGAKEFAQLIETASRLIDEAAFKVTEEGISMRAMDPSRVVLIDLNLPASIFSKYEVDGEET IGVNMDHLKKVLKRGKAKETLILRKGEENFLEISLQGTATRTFKLPLIDVEEIEVDLPELPFTAKVVILGDVIKEAVKDA SLVSDSMKFIAKENEFTMRAEGETQEVEVKLTLEDEGLLDIEVQEETKSAYGISYLSDMVKGLGKADEVTIKFGNEMPMQ MEYYIRDEGRLIFLLAPRVEE Q9UYX8 DNA polymerase II small subunit Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.069408008 1 Escherichia coli LEVO MDELVKALERAGYLLTPSAYYLLVDHFKEGKFSLVELVKFAKSKGVFIIDGDLAYEFLQFLGLGVPQEIKESYISTGEEA EKTVESQETRASELEEGGVSQVSSGELQELKEESPEISTTEEEIGGLELVQSSISTGSEVEYNNGENGESVVVLDKYGYP ILYAPEEIGEEKEYSKYEDVVIEWNPSVTPVQIEKNYEVKFDVRQVKLRPPKVKNGSGKEGEIIVEAYASLFKSRLSKLK RILRENPEISNVVDIGKLNYVSGDEEVTIIGLVNSKRETNRGLIFEVEDKTGIVKVFLPKDSEDYREAFKVLPDAVVAFK GFYSKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKAFLKFLEWLNGHVESKEEEEIVSRVKYLI IAGDVVDGIGIYPGQYSDLVIPDIFDQYEALANLLANVPEHITMFIGPGNADAARPAIPQPEFYKEYAKPIYKLKNAIII SNPAVIRLHGRDFLIAHGRGIEDVVSFVPGLTHHKPGLPMVELLKMRHLAPTFGGKVPIAPDPEDLLVIEEVPDLVQMGH VHVYDAVVYRGVQLVNSATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC Q9V2F3 2.7.7.7 DP2 subunit of D-family DNA-polymerase Pyrococcus abyssi 0.14476218799999999 1 Escherichia coli LEVO GTGDGSELPKEMEEYFEMLQREIDKAYEIAKKARAQGKDPSLDVEIPQATDMAGRVESLVGPPGVAKRIRELVKEYGKEI AALKIVDEIIEGKFGDLGSREKYAEQAVRTALAILTEGIVSAPIEGIANVKIKRNTWADNSEYLALYYAGPIRSSGGTAQ ALSVLVGDYVRRKLGLDRFKPSEKHIERMVEEVDLYHRAVTRLQYHPSPEEVRLAMRNIPIEITGEATDDVEVSHRDVPG VETNQLRGGAILVLAEGVLQKAKKLVKYIDKMGIEGWEWLKEFVEAKEKGEPKEEGKEESLAESTLEETKVEVDMGFYYS LYQKFKEEIAPSDKYAKEVIGGRPLFSDPSKPGGFRLRYGRSRASGFATWGINPATMILVDEFLAIGTQLKTERPGKGAV VTPVTTIEGPIVKLKDGSVLRVDDYNLALKVREDVEEILYLGDAVIAFGDFVENNQTLLPANYCEEWWILEFVKALKEIY EVHLEPFTENEEESIEEASDYLEIDPEFLKEMLRDPLRVKPPVELAIHFSEVLGIPLHPYYTLYWNSVEPKDVEKLWRLL KNYAEIEWSNFRGIKFAKKIVISQEKLGDSKRTLELLGLPHTVRDGNVIVDYPWAAALLTPLGNLNWEFMAKPLYATIDI INENNEIKLRDRGISWIGARMGRPEKAKERKMKPPVQVLFPIGLAGGSSRDIKKAAEEGKVAEVEIAFFKCPKCGHVGPE HLCPNCGTRKELLWVCPRCNAEYPESQAEGYNYTCPKCNVKLRPYAKRKIRPSELLNRAMENVKVYGVDKLKGVMGMTSG WKMPEPLEKGLLRAKNDVYVFKDGTIRFDATDAPITHFRPREIGVSVEKLRELGYTHDFEGKPLVSEDQIVELKPQDIIL SKEAGRYLLKVAKFVDDLLEKFYGLPRFYNAEKMEDLIGHLVIGLAPHTSAGIVGRIIGFVDALVGYAHPYFHAAKRRNC DGDEDAVMLLLDALLNFSRYYLPEKRGGKMDAPLVITTRLDPREVDSEVHNMDIVRYYPLEFYEATYELKSPKELVGVIE RVEDRLGKPEMYYGLKFTHDTDDIALGPKMSLYKQLGDMEEKVRRQLEVAKRIRAVDEHGVAEKILNSHLIPDLRGNLRS FTRQEFRCVKCNTKFRRPPLNGKCPVCGGKIVLTVSKGAIEKYLGTAKMLVTEYNVKNYTRQRICLTERDIDSLFENVFP ETQLTLIVNPNDICQRLVMARTGEVNKSGLLENLSNGSKKTEKAEKAEKPRKKSDEKPKKKRVISLEEFFSRKSK 2.7.7.7 DNA primer synthetic construct 0.0055195420000000005 1 (DC)(DG)(DC)(DC)(DG)(DG)(DG)(DC)(DC)(DG)(DA)(DG)(DC)(DC)(DG)(DT)(DG)(DC) DNA DNA template synthetic construct 0.007717934 1 (DA)(DG)(DG)(DT)(DC)(DG)(DT)(DG)(DC)(DA)(DC)(DG)(DG)(DC)(DT)(DC)(DG)(DG)(DC)(DC) (DC)(DG)(DG)(DC)(DG) DNA FE (III) ION 5.5845e-05 1 FE ZINC ION 6.5409e-05 4 ZN singleParticle particle 0.1 8.0 C-flat-2/2 4C COPPER 400 CARBON HOLEY GLOW DISCHARGE 30 AIR

5mA current

ETHANE 100 293 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.5 3.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 QUANTUM (4k x 4k) COUNTING 1-40 1 4602 5.0 40.0 1

Indicated in the M&M

Gctf PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab-initio model generated using SGD

C1 3.77 FSC 0.143 CUT-OFF RELION 3.0 149200 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_10401.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.061317734 0.10814589 0.00027422933 0.0027429883 0.83 0.83 0.83 0.014 AUTHOR ::::EMDATABANK.org::::EMD-10401:::: Post processed and masked map of the PolD-PCNA-DNA from P. abyssi emd_10401_msk_1.map emd_10401_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.011286447 0.030675715 0.0000859219 0.0017844675 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-10401:::: Unfiltered map of the PolD-PCNA-DNA from P. abyssi emd_10401_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.061317734 0.10814589 0.000085080785 0.003350669 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-10401:::: Post processed unmasked map of the PolD-PCNA-DNA from P. abyssi emd_10401_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.016221678 0.036350217 0.00007793673 0.0020641705 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-10401:::: Half map 1 of the PolD-PCNA-DNA from P. abyssi emd_10401_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.014325047 0.03554558 0.00009222483 0.002060411 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-10401:::: Half map 2 of the PolD-PCNA-DNA from P. abyssi