2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES chem_comp_atom chem_comp_bond database_2 _database_2.pdbx_DOI _database_2.pdbx_database_accession STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name PDBe PDBe 2018-09-12 2018-10-10 2019-01-30 2025-07-09 French National Research Agency ANR -17-CE11-0005 France Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA Raia P Carroni M DNA, polymerase D, Pyrococcus, REPLICATION Raia P Carroni M Henry E Pehau-Arnaudet G Brule S Beguin P Henneke G Lindahl E Delarue M Sauguet L Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. PLoS Biol. US 17 e3000122 e3000122 2019 30657780 doi:10.1371/journal.pbio.3000122 1545-7885 6hms FULLOVERLAP Complex between DNA polymerase D and DNA duplex Complex between DNA polymerase D and DNA duplex 0 1 2 3 4 DNA polymerase D 1 1 2 Pyrococcus abyssi DNA 1 3 4 Pyrococcus abyssi DNA polymerase II small subunit Pyrococcus abyssi 0.045078012 1 Escherichia coli LEVO YEVKFVEAYASLFKSRLSKLKRILRENPEISNVVDIGKLNYVSGDEEVTIIGLVNSKRETNRGLIFEVEDKTGIVKVFLP KDSEDYREAFKVLPDAVVAFKGFYSKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKAFLKFLEW LNGHVESKEEEEIVSRVKYLIIAGDVVDGIGIYPGQYSDLVIPDIFDQYEALANLLANVPEHITMFIGPGNADAARPAIP QPEFYKEYAKPIYKLKNAIIISNPAVIRLHGRDFLIAHGRGIEDVVSFVPGLTHHKPGLPMVELLKMRHLAPTFGGKVPI APDPEDLLVIEEVPDLVQMGHVHVYDAVVYRGVQLVNSATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC Q9V2F3 2.7.7.7 DNA polymerase II large subunit,DNA polymerase II large subunit Pyrococcus abyssi 0.144418969 1 Escherichia coli LEVO MELPKEMEEYFEMLQREIDKAYEIAKKARAQGKDPSLDVEIPQATDMAGRVESLVGPPGVAKRIRELVKEYGKEIAALKI VDEIIEGKFGDLGSREKYAEQAVRTALAILTEGIVSAPIEGIANVKIKRNTWADNSEYLALYYAGPIRSSGGTAQALSVL VGDYVRRKLGLDRFKPSEKHIERMVEEVDLYHRAVTRLQYHPSPEEVRLAMRNIPIEITGEATDDVEVSHRDVPGVETNQ LRGGAILVLAEGVLQKAKKLVKYIDKMGIEGWEWLKEFVEAKEKGEPKEEGKEESLAESTLEETKVEVDMGFYYSLYQKF KEEIAPSDKYAKEVIGGRPLFSDPSKPGGFRLRYGRSRASGFATWGINPATMILVDEFLAIGTQLKTERPGKGAVVTPVT TIEGPIVKLKDGSVLRVDDYNLALKVREDVEEILYLGDAVIAFGDFVENNQTLLPANYCEEWWILEFVKALKEIYEVHLE PFTENEEESIEEASDYLEIDPEFLKEMLRDPLRVKPPVELAIHFSEVLGIPLHPYYTLYWNSVEPKDVEKLWRLLKNYAE IEWSNFRGIKFAKKIVISQEKLGDSKRTLELLGLPHTVRDGNVIVDYPWAAALLTPLGNLNWEFMAKPLYATIDIINENN EIKLRDRGISWIGARMGRPEKAKERKMKPPVQVLFPIGLAGGSSRDIKKAAEEGKVAEVEIAFFKCPKCGHVGPEHLCPN CGTRKELLWVCPRCNAEYPESQAEGYNYTCPKCNVKLRPYAKRKIRPSELLNRAMENVKVYGVDKLKGVMGMTSGWKMPE PLEKGLLRAKNDVYVFKDGTIRFDATDAPITHFRPREIGVSVEKLRELGYTHDFEGKPLVSEDQIVELKPQDIILSKEAG RYLLKVAKFVDDLLEKFYGLPRFYNAEKMEDLIGHLVIGLAPHTSAGIVGRIIGFVDALVGYAHPYFHAAKRRNCDGDED AVMLLLDALLNFSRYYLPEKRGGKMDAPLVITTRLDPREVDSEVHNMDIVRYYPLEFYEATYELKSPKELVGVIERVEDR LGKPEMYYGLKFTHDTDDIALGPKMSLYKQLGDMEEKVRRQLEVAKRIRAVDEHGVAEKILNSHLIPDLRGNLRSFTRQE FRCVKCNTKFRRPPLNGKCPVCGGKIVLTVSKGAIEKYLGTAKMLVTEYNVKNYTRQRICLTERDIDSLFENVFPETQLT LIVNPNDICQRLVMARTGEVNKSGLLENLSNGSKKTEKAEKAEKPRKKSDEKPKKKRVISLEEFFSRKSK Q9V2F4 Q9V2F4 2.7.7.7 DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3') Pyrococcus abyssi 0.004635998 1 (DG)(DA)(DG)(DA)(DC)(DG)(DG)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DC) DNA DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3') Pyrococcus abyssi 0.004851129 1 (DT)(DG)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DC)(DG)(DT)(DC)(DT)(DC) DNA FE (III) ION 5.5845e-05 1 FE ZINC ION 6.5409e-05 4 ZN singleParticle particle 8.0 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 QUANTUM (4k x 4k) 1.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION
SGD ab initio
 7.1 FSC 0.143 CUT-OFF cryoSPARC 8774 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_0244.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 299.2 299.2 299.2 90.0 90.0 90.0 X Y Z -0.6584329 1.6239548 0.004671554 0.07651347 1.36 1.36 1.36 0.58 AUTHOR cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA emd_0244_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 299.2 299.2 299.2 90.0 90.0 90.0 X Y Z -3.568817 3.8639772 0.0047397213 0.42160863 1.36 1.36 1.36 AUTHOR cryo-EM half map A of DNA polymerase D from Pyrococcus abyssi in complex with DNA emd_0244_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 299.2 299.2 299.2 90.0 90.0 90.0 X Y Z -4.2714167 4.0301123 0.004843924 0.4314678 1.36 1.36 1.36 AUTHOR cryo-EM half map B of DNA polymerase D from Pyrococcus abyssi in complex with DNA