2026-09-30 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY 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_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 struct_asym struct_conn _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _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 _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 _em_admin.last_update _pdbx_struct_assembly_gen.asym_id_list _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id STRUCTURE_SUMMARY em_admin entity _chem_comp.name _chem_comp.pdbx_synonyms _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update PDBe PDBe 2025-10-04 2026-04-29 2026-04-29 2026-09-30 Max Planck Society Germany Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marburgensis (composite structure) San Segundo-Acosta P Murphy BJ Oxidoreductase, hydrogenase, dehydrogenase, polyferredoxin Segundo-Acosta PS Nomura S Fernandes-Queiroz JP Protasov E Kahnt J Kaneko M Hochberg G Shima S Murphy BJ Diversity of electron-bifurcating CO 2 -fixing supercomplexes in methanogens. Sci Adv US 12 eaed3711 eaed3711 2026 42748252 doi:10.1126/sciadv.aed3711 2375-2548 EMD-55269 focused EM volume EMD-55271 focused EM volume EMD-55272 focused EM volume EMD-55270 focused EM volume EMD-55273 focused EM volume EMD-55274 focused EM volume EMD-55286 focused EM volume EMD-55287 focused EM volume EMD-55288 focused EM volume EMD-55294 consensus EM volume 9sw6 FULLOVERLAP EMDB EMD-55269 focused EM volume EMDB EMD-55271 focused EM volume EMDB EMD-55272 focused EM volume EMDB EMD-55270 focused EM volume EMDB EMD-55273 focused EM volume EMDB EMD-55274 focused EM volume EMDB EMD-55286 focused EM volume EMDB EMD-55287 focused EM volume EMDB EMD-55288 focused EM volume EMDB EMD-55294 consensus EM volume EMDB EMD-55299 associated EM volume
Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marburgensis (composite structure)
 (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis 0 1 2 3 4 5 6 7 8 9 10 11 12 Methanothermobacter marburgensis 1.2 H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A Methanothermobacter marburgensis 0.07226496099999999 1 LEVO MAEEKKETMEEPKIGVYVCHCGVNIGGVVDVEAVRDYAAKLPNVVIAKDYKYYCSDPGQLEIQKDIKELGINRVVVAACS PRLHEPTFRRCVEEAGLNQFLFEFANIREHDSWVHMDNPEGATEKAKDLVRMAVAKARLLEPLEASKVSVDDKALVIGGG VAGIQAALDLADMGFKTYMVEKRPSISGRMGQLDKTFPTLDCSMCILAPKMVDVGKHDNIELITYAEVKEVDGYIGNFKV KIEKKPRYIDEELCTGCGSCVEVCPIEMPNYFDEGIGMTKAVYIPFPQAVPLCATIDKDYCIECMLCDEVCERGAVKHDQ EPEEIEIEVGTIIVATGYDAYDPTEKLEYGYGRHTNVITGLELERMINASGPTDGKVLKPSDGEKPKRVAFIHCVGSRDE QIGKPYCSRVCCMYIMKNAQLIKDKMPDTEVTLYYMDIRAFGKGFEEFYKRSQEKYGIKFIRGRPAEVIENPDLTLTVRS EDTLLGKVTEYDYDMVVLGVGLVPPEGAETLRQTIGLSKSADGFLMEAHPKLRPVDTLTDGVYLAGVAQGPKDIPDAVAQ ASGAAARAAIPMVKGEVEIEPIIAVTDSDVCGGCEVCIELCPFGAISIEEGHANVNVALCKGCGTCVAACPSGAMDQQHF KTEQIMAQIEAALNEPASK Q50756 1.8.98.5 H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B Methanothermobacter marburgensis 0.033496371 1 LEVO MEIAYFLGCIMNNRYPGIEKATRVLFDKLGIELKDMEGASCCPAPGVFGSFDKTTWAAIAARNITIAEDMGADIMTECNG CFGSLFETNHLLKEDEEMKAKINEILKETGREYKGEVNVRHFAEVLYNDVGLDKLSELVEKPLNLNVAVHYGCHFLKPSD EINIDNPERPTILDEIVEVTGAKSVEYKDKMMCCGAGGGVRSRDLDVALDFTREKLTNMKEAGVDAIVNVCPFCHLQFDV GQMEIKDKFGEEFDIPVLHLAQLLGLAMGLPKEDLVVDAHQVCVDECLEKLEELDRLAPGSG Q50755 1.8.98.5 H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C Methanothermobacter marburgensis 0.020548727 1 LEVO MTLLQREENIIRKGNIDKEFSEKIKAAGGDSLEYCFQCGTCTGSCPSGRRTPYRVRQIIRKANVGLKDEIISDPTLWMCT TCYSCQERCPRKVKIVDVVKLARNEAAKAGFMAPAHKAVGSFVIKTGHGVPINDATMELRKAVGLGELPPTTHQFPEALE EVQKIIKATGFDQLIGYNWETGELE Q50754 1.8.98.5 F420-non-reducing hydrogenase iron-sulfur subunit D Methanothermobacter marburgensis 0.015954442 1 LEVO MAEDDIKIVMFCCNWCSYGGADTAGTARMQYPTNIRVIRVMCSGRIEPQFVFKAFREGADGVLVTGCHHGDCHYDAGNYK LDRRMRLIYKLADELGIGRERIHHDWISASEGEKFAETVKMMVDRIRALGPSPIKKQLAEA P60238 1.12.99.- F420-non-reducing hydrogenase subunit G Methanothermobacter marburgensis 0.033786582 1 LEVO MAEKIKIGTMWLGGCSGCHLSIADFHEKLLDVMEHADFEFSPVLMDTKYDEIPELDVVVIEGGIVNDENREFAEELREKA KFVISYGTCAVYGGIPGLRNLWDKDEVIEEAYINSITTPNEEGVIPSEDVPHLEGRVKPLGEVIDVDFEVPGCPPRSDVA AEVVMALLKGEEIELPSTNLCEVCPREKPPEGLAMDFIKRQFEVGKPEDDLCLIPQGLICMGPATVSICGAECPSIAIPC RGCYGPTARVEDQGAKMISAIASDYKVEEDKTVDPEEVAEQLDDIVGTFYTFTLPAALIPMKIKKEGK P60239 1.12.99.- Tungsten formylmethanofuran dehydrogenase, subunit F Methanothermobacter marburgensis 0.038614516 2 LEVO METTEVIEGKNITVERTGEENRKLIFQDCLCAVCGLCGEICPVSAIEVNPTGAMVRTEQDESKILIDENKCVLCGMCSSI CPFQALDLQIDGTSIKELAEYPKILKSAEIDDETCIQCKACETACPQDAITITRELPERKDLITGEIEIDKDTCIYCGMC EEMCPVDAIEIEHQIPSSSSPTVATDINVDEDKCVHCGICKRICPVDAIMQVCRICPYGEYEIKVPEVTGTSYIDPELCV NCGWCQEICPVDAATVTKPFEGELIIDQDTCQACETCVMACPCNVLSFPKPEKSGEKPTKLYKDERFCIYCGACERSCPV NAIEVKRSRINTTPIKSKAWKNAFESLLK D9PU51 1.2.99.5 Tungsten formylmethanofuran dehydrogenase, subunit A Methanothermobacter marburgensis 0.06300182 2 LEVO MEYIIKNGFVYCPLNNVDGEKMDICVRDGKIVESVSDSAKVIDASGKIVMPGGVDPHSHIAGAKVNVGRMYRPEDSRRDA EKFKAGRAGSGFSVPSTFMTGYRYAQMGYTTAMEAAMPPLLARHTHEEFHDTPIIDHAAYPLFGNNWFVMEYLKEGDVDA CAAYASWLLKATKGYTI(KCX)IVNPAGTEAWGWGGNVHGIHDPAPYFDITPAEIIKGLAEVNEKLQLPHSIHLHCNDLG HPGNYETTLASFDVPKNIKANPATGERDTVLYATHVQFHSYGGTTWRDFVSEAPKIADYVNKNDHIVIDVGQITLDETTT MTADGPMEYDLHSLNGLKWANCDVELETGSGVVPFIYSARAPVPAVQWAIGMELFLLIDDPAKVCLTTDSPNAGPFTRYP RVIAWLMSNKYRMNLIEGELHKWAQRKSTIATVDREYTFSEIAQITRSTSAKVLGLSETKGHLGVGADADIAVYNINPET VDPSVDYMAIEEGFSRAAYVLKDGEIVVKDGEVVASPHGRTYWVDTRVDESTYNEVLAKVESKFKQYYSVNFANYPVQDE YLPKSAPVKGVML D9PU54 1.2.99.5 formylmethanofuran dehydrogenase subunit B Methanothermobacter marburgensis 0.048179773 2 LEVO MSVYKNVTCPVCGGSCDDIEVLYDGKTIKTRNACRMGNAKFQEMVSSHRILRPQIKTESGFRSAEWDEALDAAAEILTES KRPTLFMGSEMSTEAMAAGLELGEYLNAMVDSNATICHGPTLMGIQEAGQSAATAGEIKNRADVIIYWGTNVMDSMPRHM SRYSIFMRGFFRERGKKDRTVISVDPRETATTKASDIHLQLKPNSDYELFSALLTVIRGNEPHRSIESITGISVETIKEV ADIMLNAQFGAIYGGLGLASSEGKHRNVEMVLKLVAALNEHTKFTIGAIRGHCNVAGFNQVASWEYGFPFGVDFTRGYPR YNPGETTIVDLLQRKESDAVLVICSDLGAHLPKECVEYMKEIPVICIDIAPCPTTLVSDVVIPGVIDAMESSGTFYRFDN VPIHHKAFTTSPFPETESNEHTLRQILERVKSIKGE D9PXE7 1.2.7.12 Tungsten formylmethanofuran dehydrogenase, subunit G Methanothermobacter marburgensis 0.008564948 2 LEVO MAIGLKAYPELCHGCGNCVIACPVNALRSPEVAGGKGPTDDVEIIMIVEDGVVNIKNPDLCGKCGTCVESCPVDAIRLEE LE D9PU52 1.2.99.5 Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C Methanothermobacter marburgensis 0.043383214999999996 2 LEVO MGFVLVPKSDFQIPLEADTIRPDLFEGLDLDEIRSLQVYEGNIKRPLGEFFEIAETSHEDQLIRIDGDVSRVKYIGSGMK SGKIIINGDVGLQLGCEMKGGEIEVNGNVSSWIGMEMHGGTIKINGNAGDYVGCAYRGEWRGMKGGKIIIQGNAGNNIGG GMMAGEIYIGGDAGNFCGIRMNGGEITVRGDAGRAPGAEMVSGIIKIHGRISSLLPGFKEISTFKEDGSLMILFKGDLSE KNPEGNLYINYNKNLHILENETDEGRVITKKGIKVIYNSGSTIREGQIIKGGNKLTDDYIDECARCCISPEDYKLLGEPE NVVVSSHGNEVVLRAVEDPGIQMGTIFIPRGIWANVLTPPYTESTGSPMYKGVPVYLRKASQGERILSAEELVEEYGVGK P61937 1.2.7.12 Polyferredoxin protein MvhB Methanothermobacter marburgensis 0.04409043 1 LEVO MIVVNKEDCIRCGACQGTCPTAAIEVTPEDVIYCDICGGEPKCVDACPTGALKIEDLVVDEAGNTQGRIVFNPDKCNECG DCVEVCPPQILKLDEGKVKKIPLQGFCVMCQKCVDICPVGVIGVEGIKEPAKVELEIEGPIFIADCVGCGMCVPECPVDA ITLEKVGGVIEIDEDTCIKCGVCAQTCPWNAVYISGKKPEKRAKEIRKFELDEEACIGCNTCVEACPGDFIVPKSSNLTV ELPAICTACGLCEQLCPVDAIDLDVELGPAKPASEEGLVWDEGKCDFIGACANICPNDAIRVVTREGMKLPDNEKVDEEP SFAMCTRCGACTMACPKGALSLVDMDKVIDGEVVKRKRVQYNPALCDQCGDCIEACPYDMLKLTDEKVPLKGFCILCDQC IPACPKGALSLK P60232 F420-non-reducing hydrogenase subunit A Methanothermobacter marburgensis 0.052905050999999995 1 LEVO MVKLTMEPVTRIEGHAKITVHLDDAGNVEDTRLHVMEFRGFEKFLQGRPIEEAPRIVPRICGICDVQHHLAAAKAVDACF GFEPDDVLPAAYKMREIMNWGSYMHSHGLHFYFLAAPDFIAGKDRKTRNVFQIIKDAPDVALQAIELRKNALEIVRATGG RPIHPTSSTPGGISTELDDETQKDLLQKAQRNVELAEATLELAVPIFEENIDLVNSLGNIETYHTGLVKNGVWDVYDGIV RIKDKEGNLFREFKPADYADTIAEHVKPYSWLKFPYIKDLGYPDGVYRVSPLSRLNVADKMPDAAPKAQDYFKEFQDKFG YAQQTLLYHWARLIEVLACAECAADALEGDLSGEKFPDSLERQAGDGVGIVEAPRGTLTHHYTCDENGLITKANIVVATI QNNPAMEMGIQKVAQDYIKPGVEVDDKIFNLMEMVIRAYDPCLSCATHTIDSQMRLATLEVYDSEGDLVKRI P60227 1.12.99.- IRON/SULFUR CLUSTER 0.00035163999999999996 45 SF4 FLAVIN-ADENINE DINUCLEOTIDE 0.0007855499999999999 1 FAD Non-cubane [4Fe-4S]-cluster 0.00035163999999999996 2 9S8 FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 1 FES ZINC ION 6.5409e-05 4 ZN 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 MOLYBDENUM ATOM 9.593999999999999e-05 2 MO HYDROSULFURIC ACID 3.4081e-05 2 H2S FE3-S4 CLUSTER 0.000295795 1 F3S CARBONMONOXIDE-(DICYANO) IRON 0.00013588999999999997 1 FCO NICKEL (II) ION 5.8692999999999995e-05 1 NI water 1.8015e-05 343 HOH singleParticle particle 1.2 7.6 ETHANE FEI VITROBOT MARK IV
The buffer is pH 7.6 100 mM sodium phosphate with 150 mM NaCl, and containing 2 mM DTT
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.7000000000000001 2.4 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X FEI FALCON IV (4k x 4k) 2 18777 3.55 60.0 1 917008 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 2.7 FSC 0.143 CUT-OFF cryoSPARC
Particles had been C2-symmetry expanded. It is a composite map
722594 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD cryoSPARC 2
3D-classification without alignment with RELION used before final local refinements and CTF correction
 emd_55299.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 401.1 401.1 401.1 90.0 90.0 90.0 X Y Z -28.133669999999999 50.92418 0.012208479 0.9164779 0.835625 0.835625 0.835625 4.2 AUTHOR Composite map of the Mvh-Hdr-Fmd complex Other other
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