2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin pdbx_initial_refinement_model _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_validate_close_contact struct_conn struct_conn_type _em_admin.last_update _struct_conn_type.id PDBj PDBj 2021-02-21 2022-02-23 2022-02-23 2026-08-12 National Research Foundation (NRF, Korea) 2015M3D3A1A01064919 Korea, Republic Of Roh SH Park JS Formate dehydrogenase, ELECTRON TRANSPORT, OXIDOREDUCTASE Roh SH Park JS To Be Published 0353 7e5z FULLOVERLAP EMDB EMD-30995 associated EM volume

Formate dehydrogenase holoenzyme from Methylobacterium extorquens AM1 (MeFDH1)

Formate dehydrogenase from Methylobacterium extorquens AM1 (MeFDH1) Formate dehydrogenase from Methylobacterium extorquens AM1 (MeFDH1) 0 1 2 Methylorubrum extorquens AM1 0.07 Formate dehydrogenase alpha subunit from Methylobacterium extorquens AM1 (MeFDH1) 1 1 Methylorubrum extorquens AM1 Formate dehydrogenase beta subunit from Methylobacterium extorquens AM1 (MeFDH1) 1 2 Formate dehydrogenase Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 0.108292891 1 Methylorubrum extorquens AM1 LEVO MSNGPEPHGNKIEQPEIRADERQDAGGPANGAPSTSGGAYSQGAKSGGQAAPDPSGSYGIKDAPVAPATIAFEFDGQQVE AQPGETIWAVAKRLGTHIPHLCHKPDPGYRPDGNCRACMVEIEGERVLAASCKRTPAIGMKVKSATERATKARAMVLELL VADQPERATSHDPSSHFWVQADVLDVTESRFPAAERWTSDVSHPAMSVNLDACIQCNLCVRACREVQVNDVIGMAYRAAG SKVVFDFDDPMGGSTCVACGECVQACPTGALMPAAYLDANQTRTVYPDREVKSLCPYCGVGCQVSYKVKDERIVYAEGVN GPANQNRLCVKGRFGFDYVHHPHRLTVPLIRLENVPKDANDQVDPANPWTHFREATWEEALDRAAGGLKAIRDTNGRKAL AGFGSAKGSNEEAYLFQKLVRLGFGTNNVDHCTRLCHASSVAALMEGLNSGAVTAPFSAALDAEVIVVIGANPTVNHPVA ATFLKNAVKQRGAKLIIMDPRRQTLSRHAYRHLAFRPGSDVAMLNAMLNVIVTEGLYDEQYIAGYTENFEALREKIVDFT PEKMASVCGIDAETLREVARLYARAKSSLIFWGMGVSQHVHGTDNSRCLIALALITGQIGRPGTGLHPLRGQNNVQGASD AGLIPMVYPDYQSVEKDAVRELFEEFWGQSLDPQKGLTVVEIMRAIHAGEIRGMFVEGENPAMSDPDLNHARHALAMLDH LVVQDLFLTETAFHADVVLPASAFAEKAGTFTNTDRRVQIAQPVVAPPGDARQDWWIIQELARRLDLDWNYGGPADIFAE MAQVMPSLNNITWERLEREGAVTYPVDAPDQPGNEIIFYAGFPTESGRAKIVPAAIVPPDEVPDDEFPMVLSTGRVLEHW HTGSMTRRAGVLDALEPEAVAFMAPKELYRLGLRPGGSMRLETRRGAVVLKVRSDRDVPIGMIFMPFCYAEAAANLLTNP ALDPLGKIPEFKFCAARVVPAEAAPMAAEHHHHHH C5ATT7 1.17.1.9 Tungsten-containing formate dehydrogenase beta subunit Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 0.062397508 1 Methylorubrum extorquens AM1 LEVO MSEASGTVRSFAHPGRGRNVARAVPKGRQVDPHAKVEIEELLGTRPRQRDLLIEHLHLIQDTYGQISADHLAALADEMSL AFAEVFETATFYAHFDVVKEGEADIPRLTIRVCDSITCAMFGADELLETLQRELASDAVRVVRAPCVGLCDHAPAVEVGH NFLHRADLASVRAAVEAEDTHAHIPTYVDYDAYRAGGGYATLERLRSGELPVDDVLKVLDDGGLRGLGGAGFPTGRKWRS VRGEPGPRLMAVNGDEGEPGTFKDQLYLNTDPHRFLEGMLIGAHVVEAADVYIYLRDEYPISREILAREIAKLPEGGTRI HLRRGAGAYICGEESSLIESLEGKRGLPRHKPPFPFQVGLFNRPTLINNIETLFWVRDLIERGAEWWKSHGRNGRVGLRS YSVSGRVKEPGVKLAPAGLTIQELIDEYCGGISDGHSFAAYLPGGASGGILPASMNDIPLDFGTLEKYGCFIGSAAVVIL SDQDDVRGAALNLMKFFEDESCGQCTPCRSGTQKARMLMENGVWDTDLLGELAQCMRDASICGLGQAASNPVSTVIKYFP DLFPEPRAVAAE C5ATT6 1.2.1.2 TUNGSTEN ION 0.00018384 1 W 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE 0.000740557 2 MGD FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES IRON/SULFUR CLUSTER 0.00035163999999999996 4 SF4 FLAVIN MONONUCLEOTIDE 0.00045634399999999997 1 FMN singleParticle particle 0.5 6.4 50.0 Na2HPO4 sodium phosphate 100.0 Nacl sodium chloride 2.0 C4H10O2S2 Dithiothreitol Quantifoil R1.2/1.3 COPPER 200 GLOW DISCHARGE 40 AIR 39.0 ETHANE 100 285 FEI VITROBOT MARK IV

Blot time was for 4 seconds with 0 blot force before plunging..

This sample was monodisperse

FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 1.2 1.2 2.1 2.1 100000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 5760 4092 1 2683 3.0 50.0

Images were collected in movie-mode at

1 1471548

Topaz picking facilitated particle picking

NONE The startup model was generated by cryoSPARC ab initio processing. 4 C1 3.6 FSC 0.143 CUT-OFF cryoSPARC 2.15.0 260910 MAXIMUM LIKELIHOOD cryoSPARC 2.15.0 MAXIMUM LIKELIHOOD cryoSPARC 2.15.0 6TGA PDB experimental model FLEXIBLE FIT

A initial model was from SWISS modeling using 6TGA as a template. Initial local fitting was done using Chimera and then ISOLDE plugged in ChimeraX for flexible fitting. The model was refined by using Phenix and Coot.

Correlation coefficient REAL emd_30995_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.46921983 1.7272052 0.001371416 0.030423438 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: An electron density map of MeFDH1_aN_b holoenzyme after sharpening emd_30995_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.093844384 0.4782445 0.0021527177 0.015831139 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: An electron density map of MeFDH1 holoenzyme emd_30995_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.050223913 0.68888175 0.0035513125 0.020082867 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: A combined map of MeFDH1 holoenzyme and MeFDH1_aN_b emd_30995_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.092131995 0.7377729 0.0013714163 0.014640509 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: An electron density map of MeFDH1_aN_b holoenzyme after sharpening emd_30995_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.28284925 0.8711281 0.0021527174 0.021657424 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: An electron density map of MeFDH1 holoenzyme after sharpening emd_30995_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.38793552 0.81507003 0.0008425154 0.04980415 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: a half map of MeFDH1_aN_b (only one set of half maps could be uploaded so rest half maps were uploaded as additional EM maps with a corresponding FSC curve) emd_30995_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.40326154 0.7537626 0.0008446419 0.04979754 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: a half map of MeFDH1_aN_b (only one set of half maps could be uploaded so rest half maps were uploaded as additional EM maps with a corresponding FSC curve) emd_30995_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.68118936 0.6630404 0.001045463 0.08772967 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: a half map of MeFDH1 holoenzyme emd_30995_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 199.2 199.2 199.2 90.0 90.0 90.0 X Y Z -0.6971809 0.63969034 0.0010502484 0.087471 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-30995:::: a half map of MeFDH1 holoenzyme