2025-12-24 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update COORDINATE_REPLACEMENT AUTHOR Ligand geometry
The placement of molecule FAD head is opposite.
STRUCTURE_SUMMARY atom_site em_software entity pdbx_entity_instance_feature pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_conn_angle pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_validate_close_contact pdbx_validate_peptide_omega pdbx_validate_rmsd_angle pdbx_validate_torsion refine_ls_restr struct_asym struct_conf struct_conn struct_sheet struct_sheet_order struct_sheet_range struct_site struct_site_gen _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _em_software.category _entity.formula_weight _entity.pdbx_description _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.comp_id _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _refine_ls_restr.dev_ideal _refine_ls_restr.number _struct_asym.entity_id COORDINATE_REPLACEMENT AUTHOR Ligand geometry
The molecule of FAD is corrected.
REFINEMENT_DESCRIPTION atom_site database_2 em_software pdbx_entity_instance_feature pdbx_nonpoly_scheme pdbx_struct_assembly_prop pdbx_validate_close_contact refine _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_seq_id _atom_site.pdbx_formal_charge _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_software.category _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.comp_id _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_struct_assembly_prop.value _refine.ls_d_res_high DATA_COLLECTION chem_comp_atom chem_comp_bond STRUCTURE_SUMMARY em_admin pdbx_entry_details _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBj PDBj 2020-01-29 2020-05-27 2020-05-27 2025-12-24 Chinese Academy of Sciences XDB08020200 China National Natural Science Foundation of China (NSFC) 81520108019, 813300237 China Chinese Academy of Sciences 2017YFC0840300 China Structure of Mycobacterium smegmatis succinate dehydrogenase 2 Gao Y Gong H electron transfer chain, trimer, OXIDOREDUCTASE Gong H Gao Y Zhou X Xiao Y Wang W Tang Y Zhou S Zhang Y Ji W Yu L Tian C Lam SM Shui G Guddat LW Wong LL Wang Q Rao Z Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF. Nat Commun UK 11 4245 4245 2020 32843629 doi:10.1038/s41467-020-18011-9 2041-1723 6lum FULLOVERLAP EMDB EMD-0981 associated EM volume
Structure of Mycobacterium smegmatis succinate dehydrogenase 2
 Mycobaterium smegmatis Succinate dehydrogenase 2 Mycobaterium smegmatis Succinate dehydrogenase 2 0 1 2 3 4 5 Mycolicibacterium smegmatis MC2 51 mc2 51 0.4 Succinate dehydrogenase subunit C Mycolicibacterium smegmatis MC2 51 MC2 51 0.015644627 3 LEVO MSTQTEVPAPQPKKTRRRTLYRGDPGMWSWVLHRITGATIFFFLFVHVLDTALVRVSPQAYNEVIETYKTPIVGLMEIGL VAAVLFHALNGIRVILIDFWAKGPRYQRQMLAVIAGLFLVIFIAAVGVIGMHMVERFL Succinate dehydrogenase subunit D Mycolicibacterium smegmatis MC2 51 MC2 51 0.0192804 3 LEVO MSAPGAGESRLGRPAPVMEREHDRPAALDHPRAPRKPRGIPYFEKYAWLFMRFSGIALVFLALGHLFIMLMWQDGVYRID FNYVAERWASPFWQIWDMALLWLAMIHGANGMRTIIGDYARKNVTKFWLNSLLLLATGFTLVLGSYVLVTFDANISHHHH HHHHHH Succinate dehydrogenase subunit F Mycolicibacterium smegmatis MC2 51 MC2 51 0.003707443 3 LEVO MVLFFEILLVAAVLVITWFAVYALYRLVTDES Succinate dehydrogenase subunit A Mycolicibacterium smegmatis MC2 51 MC2 51 0.064476754 3 LEVO MIQEHRYDVVIVGAGGAGMRAAVEAGPRARTAVLTKLYPTRSHTGAAQGGMCAALANVEEDNWEWHTFDTVKGGDYLADQ DAVEIMCKEAIDAVLDLEKMGMPFNRTPEGRIDQRRFGGHTRDHGKAPVRRACYAADRTGHMILQTLYQNCVKHDVEFFN EFYALDIALTETPAGPVATGVIAYELATGDIHVFHAKAIVFATGGSGRMYKTTSNAHTLTGDGLGIVFRKGLPLEDMEFH QFHPTGLAGLGILISEAVRGEGGRLLNGEGERFMERYAPTIVDLAPRDIVARSMVLEVLEGRGAGPNKDYVYIDVRHLGE DVLEAKLPDITEFARTYLGVDPVKELVPVYPTCHYVMGGIPTTVNGQVLRDNTNVIPGLYAAGECACVSVHGANRLGTNS LLDINVFGRRAGIAAAEYAQNHNFVDMPENPAEMVVGWVGDILSEHGNERVADIRGALQQSMDNNAAVFRTEETLKQALT DIHALKERYSRITVHDKGKRYNSDLLEAIELGFLLELAEVTVVGALNRKESRGGHAREDYPNRDDTNYMRHTMAYKQGTD LLSDIRLDYKPVVQTRYEPMERKY Succinate dehydrogenase subunit B Mycolicibacterium smegmatis MC2 51 MC2 51 0.029245759999999996 3 LEVO MSAPVIDKPEAGDPELPPVPEGAVMVTLKIARFNPENPDAAGWQSFRVPCLPSDRLLNLLHYVKWYLDGTLTFRRSCAHG VCGSDAMRINGVNRLACKVLMRDMLPKNPNKQLTITIEPIRGLPVEKDLVVNMEPFFDAYRAVKPFLVTSGNPPTKERIQ SPTDRARYDDTTKCILCACCTTSCPVYWSEGSYFGPAAIVNAHRFIFDSRDEAAAERLDILNEVDGVWRCRTTFNCTEAC PRGIQVTQAIQEVKRALMFAR (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE 0.0007200119999999999 6 PEV PROTOPORPHYRIN IX CONTAINING FE 0.000616487 6 HEM MENAQUINONE-9 0.0007852329999999999 6 MQ9 CARDIOLIPIN 0.0014640429999999997 3 CDL 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE 0.000648891 3 LPP 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL 0.000836061 3 PIE FLAVIN-ADENINE DINUCLEOTIDE 0.0007855499999999999 3 FAD FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 3 FES IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 FE3-S4 CLUSTER 0.000295795 3 F3S singleParticle particle 5 7.4 100.0 NaCl sodium chloride 20.0 MOPS DVLFYONBTKHTER-UHFFFAOYSA-N 0.1 digitonin
Solutions were made fresh
 Quantifoil R1.2/1.3 COPPER 300 CARBON GLOW DISCHARGE OTHER 101.325 ETHANE 100 281 FEI VITROBOT MARK II
This sample was mono disperse.
 FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 GATAN K3 (6k x 4k) 2.0 50.0 1 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION 1 FOURIER SPACE 2.84 FSC 0.143 CUT-OFF cryoSPARC
cryoSPARC software was used for the reconstruction.
461385 COMMON LINE cryoSPARC COMMON LINE cryoSPARC cryoSPARC emd_0981.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 314.88 314.88 314.88 90.0 90.0 90.0 X Y Z -1.8452778 2.7443264 0.0005290698 0.056020573 0.82 0.82 0.82 0.15 AUTHOR emd_0981_msk_1.map emd_0981_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 314.88 314.88 314.88 90.0 90.0 90.0 X Y Z -0.46722943 1.500748 0.0012949645 0.05996803 0.82 0.82 0.82 AUTHOR emd_0981_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 314.88 314.88 314.88 90.0 90.0 90.0 X Y Z -0.46722943 1.500748 0.0012949645 0.05996803 0.82 0.82 0.82 AUTHOR