2026-09-16 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2021-01-15 2021-09-29 2021-09-29 2026-09-16 Max Planck Society Germany German Research Foundation (DFG) SH 87/1-1 Germany Japan Society for the Promotion of Science (JSPS) Japan Alexander von Humboldt Foundation Germany Pfeil-Gardiner O Watanabe T methanogenesis, flavin-based electron bifurcation, CO2-fixation, formate dehydrogenase, OXIDOREDUCTASE Watanabe T Pfeil-Gardiner O Kahnt J Koch J Shima S Murphy BJ Science US 373 1151 1156 2021 34516836 doi:10.1126/science.abg5550 1095-9203 0038 SCIEAS Afonine PV Headd JJ Terwilliger TC Adams PD Comput. Cryst. Newsl. 4 43 44 2013 9999-0018 EMD-12196 other EM volume EMD-12197 other EM volume EMD-12198 other EM volume EMD-12199 other EM volume EMD-12210 other EM volume EMD-12211 other EM volume EMD-12212 other EM volume EMD-12206 other EM volume 7bkc FULLOVERLAP EMDB EMD-12209 associated EM volume

Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (dimeric, composite structure)

EMDB EMD-12196 other EM volume EMDB EMD-12197 other EM volume EMDB EMD-12198 other EM volume EMDB EMD-12199 other EM volume EMDB EMD-12210 other EM volume EMDB EMD-12211 other EM volume EMDB EMD-12212 other EM volume EMDB EMD-12206 other EM volume PDB 7BKB unspecified PDB 7BKD unspecified PDB 7BKE unspecified Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex 0 1 2 3 4 5 6 7 8 9 10 11 12 Methanospirillum hungatei JF-1 cytoplasm 0.948 CoB--CoM heterodisulfide reductase iron-sulfur subunit A Methanospirillum hungatei JF-1 0.072885062 2 LEVO MAENTEPRIGVFVCHCGTNIAGSMSIDDVVNYAKTLPYVAVADQYQYMCSTPGQKKIDDAIKEYNLTGVVVAACSPRLHE PTFRTATKEGGLNPFRFEMANIREQNSWVHMHGMWDEATQKAKDQVRMAVAKAAKLEDLVPKSVPVEKTAMVVGGGVAGM QAALDLASAGIKTYLIERTPTIGGRMSQLDKTFPTLDCSQCILTPKMVDVGRHPNIEMMTYTEVEKVEGYIGNFDVTLRK KARGVLTPTEATAKGIVGGGCNGCGDCSAVCPVIKPNPFEMGMAPRKAIYIYHAQVMPLIYTVDFDSCVKCGLCVEACGD KKAIDLEMQDEFITVKVGTAVLATGYELFPIENKREWGYKQFDNVINALEFERLICASGPTGGHLVRPSDGKTPMKVGFV LCAGSRDNTGIGKPYCSRFCCMYSLKHAHQIMEKIPGAVAYLFYMDIRSFGKMYEEFYYRIQHEGAKFIRGRVANVLEDK ETKNLHVFTEDTLLGRPVDVEVDLLVLAAAVQPNEGANELRKKFGVSASQDGWMLEAHPKLNPCGTTTAGVFLAGVCQGP KDIPDTVAQAEGAASAASIPIHMGEVELEPYFAMCIDELCAGCGMCVNLCPYSALSLGEKNGRTVMVVTEAKCKGCGTCG GFCPGGAIKMQHFTTPQIVAQIDAFFAGGEQ Q2FKZ1 1.8.-.- F420-non-reducing hydrogenase subunit D Methanospirillum hungatei JF-1 0.015692425 2 LEVO MADDWKPQILAIICNWCSYAGADLAGGARIQYPPTVRAIRVMCTGRVDMLFILKAFVEGADGVLVSGCHFGDCHYLEGNY KAAKRMFMIKNLLRNIGLDDRRFRMTFVSASEGAKWGMVMEDVTNTIKELGPSPIKEFKK Q2FKZ0 Formate dehydrogenase, beta subunit (F420) Methanospirillum hungatei JF-1 0.04563989499999999 2 LEVO MAAKGDMLYAWAKDAEIQKKGECGGAVTALLKHALETKMVDAVVAIKKGKDLYDAVPTVITNPEDIIQTAGSLHCGTLLI PKLIKKYLNGAKDMKLAVTCKGCDAMAFYELAKRNQINLDNIIMIGVNCGGSVSPVTARKMISNKFGVDPDTVHKEEIDK GQFIIEYEGGHKGIKIDELEEEGYGRRSNCRRCKMKIPRQADIAAGNWGVIGDKAGKATFLEICSEKGANLVNSAQSKGA LEISPADPKGIDIRAKVEKAMFNLGDEWRHRDFEGMGKGKDRLKLMMSESSKCIKCYACVEACPICYCIECSTKKPWYIA PGVLPTSFMFHLIRFAHVSDSCINCGQCEELCPMEIPNALFMHSQQVEIEKMFGHIPGQDMTPPIHAFVEEKAERARLDA TGTDSIYTNIFTDE Q2FME3 1.2.99.- CoB--CoM heterodisulfide reductase subunit C Methanospirillum hungatei JF-1 0.021706963 2 LEVO MAAKSYNIPELDKKLADRRYHLSDTNPEFTQKILKTSRTIANMCYQCGTCTGSCPSAPRSSYRIRLFMRRCVLGLENEAL TDPDLWLCTTCYSCTDRCPRDIAPTDVIMAMRNLAFKRDIVPKNFLQTVQLIYNSGHGVPNNDVNRAARTKLGLPADPPT THSYPEFVKGIQKIIDHYELKENADRILKGD Q2FKZ3 CoB--CoM heterodisulfide reductase subunit B Methanospirillum hungatei JF-1 0.032930938 2 LEVO MHEYAFFLGCIAPNRYPGCEASAIKTSEKVGIKLLPLKGASCCPAPGAFGSIDLNVWYAMAARNLVLAEEMKKDIALICN GCYKSIWEVNHILKHNDELRDNVNEVLAEIDMQFKGTIDVWHLAELYYDDKVCGVQKIKDSVTTPLSGAKVAAHYGCHLM KPKKERHFGDTENPMWFEELIGALGAEPIQYRNKMQCCGAGGGVRGYDIVHALDITNEKLINIQEAGADAITELCPFCQL QFDRGQIEIKEKFGDVYNIPVLHYNELLGLAQGMSPQDLALDLHAIDCTPFLQKVL Q2FKZ2 Formate dehydrogenase Methanospirillum hungatei JF-1 0.07591144500000001 2 LEVO MSENSEIMKYVATTCPYCGVGCTLNLVVSNGKVVGVEPNQRSPINEGKLCPKGVTCWEHIHSPDRLTTPLIKKDGKFIEA SWDEALDLVAKNLKVIYDKHGPKGLGFQTSCRTVNEDCYIFQKFARVGFKTNNVDNCARICHGPSVAGLSLSFGSGAATN GFEDALNADLILIWGSNAVEAHPLAGRRIAQAKKKGIQIIAVDPRYTMTARLADTYVRFNPSTHIALANSMMYWIIKEGL EDKKFIQDRVNGFEDLKKTVENYADAEAIHGVPLDVVKDIAFRYAKAKNAVIIYCLGITELTTGTDNVRSMGNLALLTGN VGREGVGVNPLRGQNNVQGACDMGAYPNVYSGYQKCEVAENRAKMEKAWSVTNLPDWYGATLTEQINQCGDEIKGMYILG LNPVVTYPSSNHVKAQLEKLDFLVVQDIFFTETCQYADVILPGACFAEKDGTFTSGERRINRVRKAVNPPGQAKEDIHII SELAAKMGFKGFELPTAKDVWDDMRAVTPSMFGATYEKLERPEGICWPCPTEEHPGTPILHREKFATADGKGNLFGIDYR PPAEVADAEYPFTLMTGRLIFHYHSRTQTDRAADLHREVPESYAQINIEDARRLGIKNNEYIKLKSRRGETTTLARVTDE VAPGVVYMTMHFADGVNNLTNTVLDPMSKMPELKHCAISIEKVGGN Q2FRK1 1.17.1.9 Formylmethanofuran dehydrogenase Methanospirillum hungatei JF-1 0.028696901999999996 2 LEVO METITMTLVQEPELFLECYSVTPDLFAGKSLAEIADLPAHEGKIQWKLGDFFKFEGKAGETAADTKIVVNGNVRRMKRFG QQMTAGEIIINSDADMYIGGWMKGGKITVKGNADSFLGIAMEGGEILIEGDAQNHVGSAYRGDWRGMSGGLIRVKGKAGN DIGTAMTGGTIIIEGDAFIHVLTHAEGGTVIIKGDVEGRVGGQMVKGDAYILGNLLYPLPGFKKVATVEKEVDGATYTFD QFIGDLGERKEKKKGEIIYGNIFLKK Q2FRL8 1.2.7.12 Formylmethanofuran dehydrogenase, subunit G Methanospirillum hungatei JF-1 0.01638802 2 LEVO MKYRGPEDKLIVFTFYKESKKKRHFFPFFLQKISYLFQNIYLYFLTTFVQSILIDQAGATNMAFAVHVNMERCTGCNNCV VACPVNALELNTVNPSSTDKIYKVINGDAVILDVKHELCAGCGICVDACPYDVIQLSGQPPQAVEA Q2FKZ5 1.2.99.5 Formylmethanofuran dehydrogenase, subunit A Methanospirillum hungatei JF-1 0.063636211 2 LEVO MSELLIKNGYIFDPISGIKGDKADIAIKDGKIVDKVSSKAQVIDASGKTVMSGGVDIHTHVSGPKVNTGRMMRPEDKFFR GSYRGGIIKQGKRMEMGFSIPSTYKTGYAYARMGYTFTNEAAMPPLLAPHVHEEFRDTPILDQAAMPVFGNNWFCFEYIK NKELENNAAYVAWLLNATKGIGI(KCX)VVNPGGTEAWAWGENCTTINDPVPYFDITPAEIVKGLIETNEYLGLPHSVHI HGNNLGNPGNYKDTLDTLRLAESYKAKNKFGREQVLHNTHIQFHSYKGTSWADFESGAKEIMDYVNANKNITCDIGQVTL DETTTMTADGPFEYHLNQLNHIKWANVDVELETGSGVVPYIYDKNIKVCGIQWAIGLELALYAKDLMRVHITTDHPNAGP FTRYPCVIKWLMSEKARKATLDTMKWKDKVIAASNIASMDRELGLYEIAMMTRAGPAKALGLAAIYGSLVKGADGNVAIY NLDANDLPSDPELIEAAFQNTAYTIKEGVVVVKDGEIIAEPHKYTLWTKVNMPENAQVMHDIKEKFTKNYTVNLENYAVF DEHVHNPRAIELDVA Q2FRL9 1.2.99.5 Formylmethanofuran dehydrogenase, subunit D Methanospirillum hungatei JF-1 0.015157499 2 LEVO MKAKKTLNMITQRAVEEGIAMEIGKTSRQYFDACSIIEMNEQDMKELGIMKNTNVRVKSESGEVVVKAVVGRQTCYPGLC HIRQGVWANQVVPPRTQSTGAPQYSGFPVTVEPVPNERLKTALELVQGAVGMWKGDQ Q2FRF6 1.2.99.5 Formylmethanofuran dehydrogenase, subunit F Methanospirillum hungatei JF-1 0.04221673399999999 4 LEVO MSTLFPKYSKTTDGSKVIMEQRLLQQVNNLILDNDICTGCGICSEVCPEEAISVGAVGGVRRGLVDDAASIHVDETKCSY CGVCVIMCPFSALALKVDGEERLPILEKEGFPTYDKGTAIDQDKCVRCNICDDVCPRDAIDRDVPLFEGEDKEGLAKGQA VELKIEFKVDDEKCTKCGICGNLCEAINVLHKPFSPEIGKVEGEVIWDEAYCDGCNVCAEACPSEAIKVTRTVVGQKKLG NVNIIDEDCCTCRWCAINCPTEAITVNKIFEGEITFHAEKCPGGCSTCVDVCPANAIYLPTPKPAKDMKGQIEAKIAVNK DFCILCGACVNACPGEDIIYLRRDSVKIKGKETDLFKKIKEKLFTPRTSKVKEQPSLAGSVELKAVSQ Q2FKZ4 1.2.99.5 Formylmethanofuran dehydrogenase, subunit B Methanospirillum hungatei JF-1 0.049371586 2 LEVO MPKVIENVGCPYCGCSCDDVRITVSDDGKDILEVENVCAIGTEIFKHGCSKDRIRLPRMRQPDGSMKDISYEEAIDWTAR HLLKAKKPLMYGFGSTNCEGQAAAARVMEIAGGMLDNCATICHGPSFLAIFDNGYPSCTLGEVKNRADVIVYWGSNPAHA HPRHMSRYSIFPRGFFTGKGQKKRTVIVIDPRFTDTANVADYHLQVKQGHDYELFNAFRMVIHGHGKDLPDEVAGIKKET ILEVAEIMKNARFGTTFFGMGLTHTDGRNHNIDIAISLTRDLNKISKWTIMAMRGHYNIAGPGVVWSWTFGFPYCLDLTK QNHAHMNPGETSSVDMAMRDEVDMFINIGTDAAAHFPIPAVKQLKKHPWVTIDPSINMASEISDLHIPVCICGVDVGGIV YRMDNVPIQFRKVIEPPEGVMDDETLLNKIADRMEELKAKGEA Q2FRM0 1.2.99.5 IRON/SULFUR CLUSTER 0.00035163999999999996 48 SF4 FLAVIN-ADENINE DINUCLEOTIDE 0.0007855499999999999 4 FAD FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES Non-cubane [4Fe-4S]-cluster 0.00035163999999999996 4 9S8 ZINC ION 6.5409e-05 4 ZN MOLYBDENUM ATOM 9.593999999999999e-05 2 MO 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 4 MGD singleParticle particle 0.5 7.6 25.0 Tris-HCl Tris-HCl C-flat-2/1 COPPER 300 GLOW DISCHARGE 45 AIR 0.038

15mA

ETHANE 70 293 HOMEMADE PLUNGER

Preparation in an anaerobic tent (O2 < 20 ppm at all times, nearly always < 2ppm)

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 8745 50.0 1

Recorded in counted mode

CTFFIND 4.1.13 RELION 3.1 PHASE FLIPPING AND AMPLITUDE CORRECTION

ab initio model generation, stochastic gradient descent, Relion 3

C2 3.0 FSC 0.143 CUT-OFF RELION 3.1

As this is a composite map, the resolution is estimated from the resolutions for masked refinements of several regions, which range from 2.6 to 3.7 A.

1239454 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 OTHER