Strand displacement state III of Human mitochondrial DNA polymerase gamma ternary complex

2026-04-01 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Ligand identity STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond em_admin em_software entity entity_poly entity_poly_seq ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_contact_author pdbx_entity_instance_feature pdbx_poly_seq_scheme pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list pdbx_struct_sheet_hbond pdbx_validate_rmsd_angle pdbx_validate_torsion struct_conf struct_conn struct_conn_type struct_sheet_range _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _em_admin.last_update _entity.formula_weight _entity.pdbx_description _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly_seq.mon_id _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.hbond_type_12 _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.stretch _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_struct_assembly.details _pdbx_struct_conn_angle.value _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_3 _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_seq_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_seq_id STRUCTURE_SUMMARY em_admin em_software entity entity_poly _chem_comp.name _em_admin.last_update _entity.formula_weight _entity.pdbx_description _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code RCSB RCSB 2025-09-03 2026-02-18 2026-02-18 2026-04-01 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States Strand displacement state III of Human mitochondrial DNA polymerase gamma ternary complex Park J Yin YW DNA polymerase gamma, strand displacement, mitochondria, TRANSFERASE-DNA complex Baruch-Torres N Park J Mora-Garduno J Roy A Singh A Cisneros GA Brieba LG Patel SS Yin YW Pol gamma possesses separate metal binding sites for polymerase and strand displacement functions. Biorxiv US 2026 41648309 doi:10.64898/2026.01.25.701366 2692-8205 9y4e FULLOVERLAP EMDB EMD-72480 associated EM volume

Ternary complex of human mitochondrial DNA polymerase gamma bound to dumbbell DNA and dATP Ternary complex of human mitochondrial DNA polymerase gamma bound to dumbbell DNA and dATP 0 1 2 3 Homo sapiens DNA polymerase subunit gamma-1 Homo sapiens 0.13962867199999998 1 Insect cell expression vector pTIE1 LEVO MSRLLWRKVAGATVGPGPVPAPGRWVSSSVPASDPSDGQRRRQQQQQQQQQQQQQPQQPQVLSSEGGQLRHNPLDIQMLS RGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAVPLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQA QLPPKPPAWAWAEGWTRYGPEGEAVPVAIPEERALVFAVAVCLAEGTCPTLAVAISPSAWYSWCSQRLVEERYSWTSQLS PADLIPLEVPTGASSPTQRDWQEQLVVGHNVSFDRAHIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKH KVQPPTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDV WATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQLLSGERYK EDPWLWDLEWDLQEFKQKKAKKVKKEPATASKLPIEGAGAPGDPMDQEDLGPCSEEEEFQQDVMARACLQKLKGTTELLP KRPQHLPGHPGWYRKLCPRLDDPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRRDNLAKLPTGTTL ESAGVVCPYRAIESLYRKHCLEQGKQQLMPQEAGLAEEFLLTDNSAIWQTVEELDYLEVEAEAKMENLRAAVPGQPLALT ARGGPKDTQPSYHHGNGPYNDVDIPGCWFFKLPHKDGNSCNVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISF WRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQA PPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQP FAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWYRLSDEGEWLVRELNLPVDRTEGGWISLQDLRKVQRETARKSQWKK WEVVAERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLF EEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTMDCKTP SNPTGMERRYGIPQGEALDIYQIIELTKGSLEKRSQPGP P54098 2.7.7.7 DNA polymerase subunit gamma-2, mitochondrial Homo sapiens 0.054991 2 Escherichia coli BL21(DE3) LEVO MRSRVAVRACHKVCRCLLSGFGGRVDAGQPELLTERSSPKGGHVKSHAELEGNGEHPEAPGSGEGSEALLEICQRRHFLS GSKQQLSRDSLLSGCHPGFGPLGVELRKNLAAEWWTSVVVFREQVFPVDALHHKPGPLLPGDSAFRLVSAETLREILQDK ELSKEQLVAFLENVLKTSGKLRENLLHGALEHYVNCLDLVNKRLPYGLAQIGVCFHPVFDTKQIRNGVKSIGEKTEASLV WFTPPRTSNQWLDFWLRHRLQWWRKFAMSPSNFSSSDCQDEEGRKGNKLYYNFPWGKELIETLWNLGDHELLHMYPGNVS KLHGRDGRKNVVPCVLSVNGDLDRGMLAYLYDSFQLTENSFTRKKNLHRKVLKLHPCLAPIKVALDVGRGPTLELRQVCQ GLFNELLENGISVWPGYLETMQSSLEQLYSKYDEMSILFTVLVTETTLENGLIHLRSRDTTMKEMMHISKLKDFLIKYIS SAKNV Q9UHN1 2.7.7.7 DNA (77-MER) synthetic construct 0.023791139 1 (DG)(DC)(DT)(DT)(DT)(DT)(DC)(DT)(DG)(DG)(DT)(DG)(DA)(DA)(DA)(DA)(DG)(DC)(DT)(DG) (DG)(DT)(DC)(DG)(DG)(DC)(DA)(DG)(DC)(DG)(DC)(DT)(DT)(DG)(DA)(DG)(DC)(DA)(DG)(DC) (DG)(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DG)(DC)(DT)(DG)(DC)(DC)(DG)(DC)(DT)(DG) (DC)(DT)(DC)(DA)(DA)(DG)(DC)(DG)(DC)(DT)(DG)(DC)(DC)(DG)(DA)(DC)(DOC) DNA CALCIUM ION 4.0078e-05 1 CA 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE 0.000491182 1 DTP singleParticle particle 7.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 GATAN K3 BIOQUANTUM (6k x 4k) 49.6 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.05 FSC 0.143 CUT-OFF cryoSPARC 120657 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_72480.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 275.2 275.2 275.2 90.0 90.0 90.0 X Y Z 0.0 26.05172 0.21047126 0.73410803 0.86 0.86 0.86 2.53 AUTHOR ::::EMDATABANK.org::::EMD-72480:::: emd_72480_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 275.2 275.2 275.2 90.0 90.0 90.0 X Y Z -0.3207916 0.5840364 0.00040983548 0.036693107 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-72480:::: emd_72480_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 275.2 275.2 275.2 90.0 90.0 90.0 X Y Z -0.32611927 0.5969532 0.0004153406 0.036468867 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-72480::::