2025-07-02 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_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _em_admin.last_update DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name PDBe PDBe 2024-08-13 2025-04-16 2025-04-16 2025-07-02 Swedish Research Council Sweden Knut and Alice Wallenberg Foundation Sweden Cancerfonden Sweden Structure of WT human mitochondrial DNA polymerase gamma Valenzuela S Falkenberg M Mitochondrial DNA polymerase, activator, TRANSFERASE/DNA, TRANSFERASE-DNA complex Valenzuela S Zhu X Macao B Stamgren M Geukens C Charifson PS Kern G Hoberg E Jenninger L Gruszczyk AV Lee S Johansson KAS Miralles Fuste J Shi Y Kerns SJ Arabanian L Martinez Botella G Ekstrom S Green J Griffin AM Pardo-Hernandez C Keating TA Kuppers-Munther B Larsson NG Phan C Posse V Jones JE Xie X Giroux S Gustafsson CM Falkenberg M Small molecules restore mutant mitochondrial DNA polymerase activity. Nature UK 642 501 507 2025 40205042 doi:10.1038/s41586-025-08856-9 1476-4687 0006 NATUAS EMD-51326 other EM volume EMD-51327 other EM volume EMD-51328 other EM volume EMD-51329 other EM volume 9ggf FULLOVERLAP Structure of WT human mitochondrial DNA polymerase gamma Structure of WT human mitochondrial DNA polymerase gamma 0 1 2 3 4 Homo sapiens DNA polymerase subunit gamma-1 Homo sapiens 0.138044641 1 Spodoptera frugiperda LEVO MHHHHHHVSSSVPASDPSDGQRRRQQQQQQQQQQQQQPQQPQVLSSEGGQLRHNPLDIQMLSRGLHEQIFGQGGEMPGEA AVRRSVEHLQKHGLWGQPAVPLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTRY GPEGEAVPVAIPEERALVFDVEVCLAEGTCPTLAVAISPSAWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTGASSPTQ RDWQEQLVVGHNVSFDRAHIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARR GPAISSWDWLDISSVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLFLERC PHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQK KAKKVKKEPATASKLPIEGAGAPGDPMDQEDLGPCSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCP RLDDPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRRDNLAKLPTGTTLESAGVVCPYRAIESLYRK HCLEQGKQQLMPQEAGLAEEFLLTDNSAIWQTVEELDYLEVEAEAKMENLRAAVPGQPLALTARGGPKDTQPSYHHGNGP YNDVDIPGCWFFKLPHKDGNSCNVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPR SALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQAPPGYTLVGADVDSQELWI AAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEA AEKAQQMYAATKGLRWYRLSDEGEWLVRELNLPVDRTEGGWISLQDLRKVQRETARKSQWKKWEVVAERAWKGGTESEMF NKLESIATSDIPRTPVLGCCISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVR YLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEAL DIYQIIELTKGSLEKRSQPGP P54098 2.7.7.7 DNA polymerase subunit gamma-2 Homo sapiens 0.053229684
A169T (Single Nucleotide Polymorphism)
2 Spodoptera frugiperda LEVO MDAGQPELLTERSSPKGGHVKSHAELEGNGEHPEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDSLLSGCHPGFGPLGV ELRKNLAAEWWTSVVVFREQVFPVDALHHKPGPLLPGDSAFRLVSAETLREILQDKELSKEQLVTFLENVLKTSGKLREN LLHGALEHYVNCLDLVNKRLPYGLAQIGVCFHPVFDTKQIRNGVKSIGEKTEASLVWFTPPRTSNQWLDFWLRHRLQWWR KFAMSPSNFSSSDCQDEEGRKGNKLYYNFPWGKELIETLWNLGDHELLHMYPGNVSKLHGRDGRKNVVPCVLSVNGDLDR GMLAYLYDSFQLTENSFTRKKNLHRKVLKLHPCLAPIKVALDVGRGPTLELRQVCQGLFNELLENGISVWPGYLETMQSS LEQLYSKYDEMSILFTVLVTETTLENGLIHLRSRDTTMKEMMHISKLKDFLIKYISSAKNVHHHHHH Q9UHN1 DNA (primer strand) synthetic construct 0.0077649979999999995 1 (DG)(DC)(DA)(DT)(DG)(DC)(DG)(DG)(DT)(DC)(DG)(DA)(DG)(DT)(DC)(DT)(DA)(DG)(DA)(DG) (DG)(DA)(DG)(DC)(DC) DNA DNA (template strand) synthetic construct 0.012162782999999998 1 (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DT)(DC)(DC)(DG)(DG)(DG)(DC)(DT)(DC) (DC)(DT)(DC)(DT)(DA)(DG)(DA)(DC)(DT)(DC)(DG)(DA)(DC)(DC)(DG)(DC)(DA)(DT)(DG)(DC) DNA CALCIUM ION 4.0078e-05 1 CA 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE 0.00046715699999999995 1 DCP singleParticle particle 7.5 ETHANE FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.2 105000.0 GATAN K3 BIOQUANTUM (6k x 4k) 40.0 1 cryoSPARC 4.3.1. PHASE FLIPPING AND AMPLITUDE CORRECTION
Ab-initio model
 C1 2.65 FSC 0.143 CUT-OFF cryoSPARC 4.3.1. 821488 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1. MAXIMUM LIKELIHOOD cryoSPARC 4.3.1. emd_51330.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -28.956099999999999 47.320700000000002 0.0018176454 0.9749231 0.825 0.825 0.825 3.5 AUTHOR emd_51330_msk_1.map emd_51330_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.25220972 0.5148465 0.00013752404 0.014548546 0.825 0.825 0.825 AUTHOR Unsharpened map emd_51330_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.0017662782 1.712223 0.0015146016 0.026383836 0.825 0.825 0.825 AUTHOR DeepEMhancer map emd_51330_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.2813118 0.64430165 0.00055807387 0.021119189 0.825 0.825 0.825 AUTHOR cryoSPARC half map A emd_51330_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.29016578 0.56758714 0.00055817695 0.021110136 0.825 0.825 0.825 AUTHOR cryoSPARC half map B