2026-09-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation em_admin pdbx_database_related _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _em_admin.last_update _pdbx_database_related.db_id EXPERIMENTAL_SUMMARY citation em_admin pdbx_database_related _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _em_admin.last_update _pdbx_database_related.db_id DATABASE_REFERENCES citation citation_author em_admin _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_entity_instance_feature pdbx_entity_nonpoly pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_nonpoly_scheme pdbx_struct_assembly_gen pdbx_struct_conn_angle pdbx_validate_close_contact struct_asym struct_conn _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_comp_id _atom_site.label_entity_id _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type _chem_comp_atom.atom_id _chem_comp_atom.comp_id _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.type_symbol _em_admin.last_update _pdbx_entry_details.has_protein_modification _pdbx_struct_assembly_gen.asym_id_list STRUCTURE_SUMMARY em_admin entity _chem_comp.name _chem_comp.pdbx_synonyms _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-10-22 2026-07-01 2026-07-01 2026-09-09 German Research Foundation (DFG) 505997786 Germany European Research Council (ERC) 101075992 European Union Paul S Schuller JM Methanogenesis, Super-assembly, Flavin-based electron bifurcation, heterodisulfide-reductase, polyferredoxin, formylmethanofuran dehydrogenase, electron transport, oxidoreductase Paul S Pascoa TC Klamke MA Bohn S Abendroth F Deobald D Vazquez O Stripp ST Schuller JM Nature UK 656 1054 1063 2026 42420451 doi:10.1038/s41586-026-10744-9 1476-4687 0006 NATUAS EMD-54996 consensus EM volume EMD-54999 focused EM volume EMD-55424 focused EM volume EMD-55426 focused EM volume 9t1s FULLOVERLAP EMDB EMD-55451 associated EM volume

Heterodisulfide-Hydrogenase-Formate Dehydrogenase dimer

EMDB EMD-54996 consensus EM volume EMDB EMD-54999 focused EM volume EMDB EMD-55424 focused EM volume EMDB EMD-55426 focused EM volume Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly 0 1 2 3 4 5 6 7 9 8 Methanococcus maripaludis S2 8 CoB--CoM heterodisulfide reductase iron-sulfur subunit A Methanococcus maripaludis deltae 0.071360758 2 LEVO MSDPKVGVFVCYCGANINGAVDCEAVKDFASELDGVAVAATYPFMCADPGQGLIKDAIKEHGLDRIVVAACTPKIHEPTF RGCLQDAGISPYYLEFVNIREHDAFVHMGDVEGATRKACEMIAGGVERAKKLEDVPQKVVDVDKSCMVIGAGIAGIQSAL DLGDQGFKVYLVDKDESIGGRMAQLAKTFPTDDCAMUILAPKMVSAANHPNIELITFAEIKNIDGYIGNFDVTLEKKPRY VDEDTCTGCGACAAACPIEVPNEFDLGLGTRKAIYVPFPQAVPLLYTIDKEHCIDCGLCAKVCCAEAVRYDQKPQELNIK VGTIITATGYDEFDATKKEEYGYGVYDNVITTLEVERMINPAGPTHGHEIRPSDGKAPKRTVYIQCVGSRDEKVGNPYCS RVCCMFALKNAQLMKMHDPNAEVYICYMDIRAFGKGYEEYYKRAQDQFGVKFIRGRPANIFEDPETKNLTVRVEDTLMGE ILEIDADLVVLSAGLEAKKDAGELAKMLGIDRGPEGFFKELHPKLAPVNTKVDGIAIAGVAQGPKDIPDTVAQAKGAASA VAIPMSQGQFKIEMIRATVNEEVCGGCKVCALMCPYNAITYEEKDGHLVAITDDVACKGCGACAAACPSGAMQLRYYRDE QVIGMIDGILNAAKMLEE A0A2L1CB19 1.8.-.- Heterodisulfide reductase subunit B Methanococcus maripaludis deltae 0.032062203 2 LEVO MKYAFFLGCIMPNRYAGVESATRTVMEKLGVELVDMPGASCCPAPGVFGSFDQKTWLTLAARNLVIAEEMGTDIVTVCNG CYGSLYEAAHMLHENKEALAMVNEQLKEIGKEYKGTVHVRHFAELIYKEIGVDKIRENVVKPLAVNIGVHYGCHFLKPTA AKGLGNAEHPTMLDELVEATGAKSVDYKDKMMCCGAGGGVRAKELDLALSMTQEKIENMLAVGADATVNVCPFCQLQFDR GQVEIKEKLGNEYNFPVVHLSQLLGLAMGMDPKEVALDVNFISPEPLLQKLGY A0A7J9NT94 1.8.98.1 H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2 Methanococcus maripaludis deltae 0.020483849999999998 2 LEVO MMKAEELNKGFVNEIIEAGTPVPGEKEVASLKSCYQCGTCTGSCPSGRRTAYRTRKVIRQALLGIDSVLDSDDIWKCTTC YTCYERCPRDVKVTEIIKTIRNLAAQKGNMAKPHKMTAVYVLKAGHAVPANDDTAKLRKSIGLAEKAPIAQFSQKDMDEL RTLAKNLKFDELIGFDWKTMGLKQ Q6LYD7 1.8.98.5 Coenzyme F420-reducing hydrogenase, alpha subunit Methanococcus maripaludis deltae 0.045687258 1 LEVO MGKVTIEPLSRLEGHGKVSITLDDAGKPTDVKLHITALRGFEQFVVGRPAEEVPRIVPRICGICQTPHHLASVKAVDAAW GAEVPSAAEKLRELMHLGNMMHSHALHFYYLAAPDFVLGPDSDPAARNIIGVIGAAPEVAKKAIAMRRVGQSIVETIGGR AIHPVTGVPGGVSKALSEEKRDELLKEIDEMIAYGQDGIALIKSLNEKYMDVVKSLGVIDTWYLGMVKEGKHNFYGDTLR FMSPDGKQTTDFKPSEYLDNIGEHVVGHNYVKYPYNKKVGYPDGLYRVGPLAMLNVCDSMPTPLAEEARKDFADTFGKPA NQSLAYNHARLIELLASCERVKELLEDSEITSTDIKAEVEPKAGNGVGAIYAPRGTLFHNYETDDKGIVVKANMIVASTH NVPTMEKAIQQAAEVVFK A0A2L1CAX5 1.12.1.2 F420-non-reducing hydrogenase small subunit Methanococcus maripaludis deltae 0.030787497999999996 1 LEVO MADKVKVGIIQLCGCSGCHISLLDLHEGLLDVLPALEIVYAPIIADVKEIPDVDVFLVEGGVRSEHDEHLIHEIREKSKV VIAWGSCAAFGGIPGLGNMYTPEQLKETVYTTVSTDNPGVIPTEGVPELTTEVRAIPDVVKADYVIPGCPPKPALTAGAI VALLEGKDPVLPTKIVCDECPRTKENVFPKEFKRSFEGTPDPEKCLFEQGYTCMGMATRAGCGAMCPSANMPCRGCYGKT DETLDQGAAAANTYANAGEAALEIPDKVATLNRFTLPVALVSKKIQKE A0A7J9P3N2 1.12.99.- F420-non-reducing hydrogenase subunit delta Methanococcus maripaludis deltae 0.014675697 2 LEVO MAEPVIMAFVCYQUGYGAADLAGTSRMQYPASVRAIRVPCTGKFDITYALRAFQKGADAVFVAGUKPNECAFETGNFKAE ERVKFGKQILDELGIGGERLEMFFMSGADAGKFTEAVKEMTDRVKKLGPNPIKA A0A2L1CBC1 F420 non-reducing hydrogenase subunit Methanococcus maripaludis deltae 0.003119515 1 LEVO MVDEAKLNLIEIVLRAYDPUYSCAAHM A0A2L1CB29 formate dehydrogenase (coenzyme F420) Methanococcus maripaludis deltae 0.074353594 1 LEVO MELDFIHTICPYCGTGCGVDLVVKDGTLVGTNPFKRHPVNEGKTCIKGSYCHEFVHRDDRLKTPLIRKNGELVEASWDEA LELISGKLQNYSPEEVGFFSSARCTNEDNYVFQKFARTVIKTNNVDHCARLUHSATVVGLGQAFGSGAMTNSISDIEDAD CIFIIGSNTFEQHPLIARRVVRAKEKGTKIIVIDPRYTPTAKQADLYLQLLPGTNIAVLNAIMHVLVKENLVDEEFIKNR TKGYEELKQTLETYTPEYASKLSGVSPELIVEAAKMYGSANAASILYCMGITQFTTGVNNVKSCCNLAMITGNIGKPGTG VNPLRGQNNVQGACDMGALPNVFPGYQAVPANHEKYAEAWNTCVDPNVGLSIPDMLAKAGEQVKCIYVMGENPMVSDPDI HHVEHALKSLDLLIVQDIFLTETAQVADVVLPGASWAEKDGTFSNTERRIQKINKAVDSPGEAIADWKIVKMLAEKMGQG ELFNFNTAEEVFQEIAKVTPQYAGVTYERLGVDGLHWPCKTCEDPGTPILHCEKCLTPDGLGNIFAIDYADPDEMADSEY PMTLTTGRIIFHYHTGTMTRRSKHMADEINEGFVEIHPEDAEKMGIKNKQKVKVSTRRGEVVVNAKITPNIKQGVVFMPF HFAETAANILTNPAQDPNCKIPEYKVCAAKVEKI M9QXF8 1.17.98.3 formate dehydrogenase (coenzyme F420) Methanococcus maripaludis deltae 0.042748421999999994 1 LEVO MSNEMYYVQASDPAILEKGECGGAVTALFKYLLDKGIVDGVLALKKGVDVYDAIPTFVTSSEDLLSTAGSLHCAPTMWGG IIKEYLQDAKIAVPVKPCDMRAIVELAKRAQINLDNVYMIGLNCGGTVPPKTAMEMIKLFYEVDPKDVVKEEIDKGKFII VMKDGSHKEVKMHDLEDNGYGRRVNCQRCDEKIPRKADIAAGNWGVIGEDAGKYTFMEVCTEKGKQLLESAEKDGYIKKK APNPKGLEIRAKVESSMLKMGEDYKRKWLEEEYPSIEEWNRQWNKCIKCYGCRDVCPVCFCRDCALTADYVDTGSIPPDP IMFQGVRMSHMAFSCVNCGQCEDVCPMEIPVARIFHKIQEKTRKELGYRPGVDDEAPPALGGS A0A7J9PDY4 1.17.98.3 IRON/SULFUR CLUSTER 0.00035163999999999996 24 SF4 FLAVIN-ADENINE DINUCLEOTIDE 0.0007855499999999999 3 FAD Non-cubane [4Fe-4S]-cluster 0.00035163999999999996 4 9S8 CARBONMONOXIDE-(DICYANO) IRON 0.00013588999999999997 1 FCO NICKEL (II) ION 5.8692999999999995e-05 1 NI FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES 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 singleParticle particle 7.6 25.0 C8H18N2O4S HEPES 100.0 NaCl sodium chloride 12.5 MgCl2 magnesium chloride 20.0 C27H33N9O15P2 flavin adenine dinucleotide Quantifoil R2/1 COPPER 300 ETHANE-PROPANE 100 279 FEI VITROBOT MARK IV

Vitrification under strict anaerobic conditions inside a Coy Lab's vinyl anaerobic chamber (95% N2/ 5% H2).

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 2.0 FEI FALCON IV (4k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 4.0 FSC 0.143 CUT-OFF cryoSPARC 110231 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION