Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP

2026-09-02 REL PDBe 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 INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_validate_close_contact struct_conn _chem_comp.formula _em_admin.last_update PDBe PDBe 2024-10-09 2025-02-26 2025-02-26 2026-09-02 European Research Council (ERC) 101075992 European Union Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP Ramirez-Amador F Paul S Kumar A Schuller JM Methyl-coenzyme M reductase, activation complex, ATPase, Iron-sulfur clusters, OXIDOREDUCTASE Ramirez-Amador F Paul S Kumar A Lorent C Keller S Bohn S Nguyen T Lometto S Vlegels D Kahnt J Deobald D Abendroth F Vazquez O Hochberg G Scheller S Stripp ST Schuller JM Structure of the ATP-driven methyl-coenzyme M reductase activation complex. Nature UK 642 814 821 2025 40240609 doi:10.1038/s41586-025-08890-7 1476-4687 0006 NATUAS 9h1l FULLOVERLAP PDB 8S7V unspecified

MCR activation complex + A2

PDB 8S7X unspecified

MCR activation complex

EMDB EMD-51767 associated EM volume

Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP

Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP 0 1 2 3 4 5 6 7 8 9 Methanococcus maripaludis 0.5 UPF0288 protein MmarC6_0796 Methanococcus maripaludis 0.056520800999999996

Methanogenesis marker protein 3

1 LEVO MNVLVNNNPKSGKTLEDVIKDEYYIPGSNIVIIKGTATVIKEETKKYLIKTTKGSFVVGITEENETVDFWNKNYKSFEDK SLIWKSISDVSFGSIEIPLPVSSVKQNFKKWDVVLSVSGLDTSEGNLIFVQRDVLELYGLENPKIGILIGGKRVLKTLTA DDRIISIEQMRESKENIDYEITTNLNKEIQDTWKIYTYCKAEFDGPPQSTEHALAILENGTLEISENTNTYVADCRLQTL FIDEENPEDRDRGTITVRNIGNGVGKVYIYQESRASSLSHTVVGKVTDGIEIVDFSNSGHITVKTNPERLSVIGKTQKDA KILFEKHGITLKMEGNIDEDAIIVEQVPEYTMDILKSKEVTTKGIEPEKLLYVEIYDKDAPTTSWYFRKVTGLTTKRIGT LKIYFKHDDISMFERDWDYSKGLLPENTPEKSIDSGIIAVTNMVKKYKGYIGVRTSSNDKYGPTGETFEGTNIVGKVVKN SEILKSVKQGENIYILEVNSN A9A8E0 Methyl-coenzyme M reductase subunit gamma Methanococcus maripaludis 0.029665488

Methyl-coenzyme M reductase subunit gamma

2 LEVO MAYTPQFYPGATKVAENRRNHLNPNYELEKLREIPDEDVVKIMGHRQPGEDYKTVHPPLEEMDFVEDYARDLVEPLNGAK EGHRVRYIQFADSMYFAPAQPYDRSRSYMSRLRGVDAGTLSGRQVVECRESDLEEFSKNILMDTELFDPATSGMRGATVH GHSLRLDENGMMFDALQRCVFDEKTGHVMYVKDQVGKPLDAPVDVGEPIPEAKLREITTIYRNDGVAMRADPDVIEVVKR IHRARTLGGYIPTNETFKGL A0A2L1CBG2 2.8.4.1 Methyl-coenzyme M reductase subunit beta Methanococcus maripaludis 0.046701203

Methyl-coenzyme M reductase subunit beta

2 LEVO MVKYEDKISLYDAKGNLVAENVPLEAISPLYNPTIKSMVKNIKRTVAVNLAGIEGTLAAGKIGGKGCQVPGRTLDISAVS NAQAIADEVEKILKVSEDDDTAVKIINGGKQLAVQVPTARLEVAAEYSVSMLSTAMALKEALIKTFNIDMFDGSTVHAAI VGNYPQVMDYAGGNIASLLGAPSMMEGLGYALRNIPVNHAVATTKKNMMNAIAFSSVMEQTATFEMGDAVGSFERQHLLG LAYQGLNADNLVIDFIKANAKGTVGSVVETVIDRAIADGVIVVDKTMSSGFNMYKPADVNKWNAYAAAGLVAAVAVSCGA ARAAQNVASVILYFNDILEYETGLPGVDYGRSMGTAVGFSFFSHSIYGGGGPGIFNGNHVVTRHSKGFAIPPVCAAMCAD AGTQMFSPEHTSGLVGSVYSAFDEFREPMKYVIEGALSIKDQF A0A2L1CBB3 2.8.4.1 Methyl-coenzyme M reductase subunit alpha Methanococcus maripaludis 0.061230703

Methyl-coenzyme M reductase subunit alpha

2 LEVO MEAEKRLFLKALKEKFEEDPKEKYTKFYTFGGWEQSARKREFVEANEKIVSEKRQGIPLYNPDIGVPLGQRKLMPYKLSN TDDYCEGDDLHFLNNAAIQQLWDDIRRTVIVGMDTAHSVLEKRLGVEVTPETINEYMHTINHSLPGGAVVQEHMVEVHPS LAWDCYARIFTGDDELADELDSRFLIDINKLFPEEQAETLKAAIGKKTYQVSRVPSLVGRVCDGGTISRWSAMQIGMSFI TAYKLCAGEAATADFSYASK(MHS)ADVIQMGNALPGR(AGM)ARGPNEPGGIRFGILSDVVQTTRVSEDPVEQSLEVVA TGAALYDQIWLGAYMSGGIGFTQYATASYTDDILDDFSYYALDYVEKKYGRMGTKATMDVVEDVAGEVTLYALEQYDDYP ALLEDHFGGS(MGN)RAAVAAAASGIGVCMATGNSNAGVNGWYLSQILHKEYHSRLGFY(GL3)YDLQDQ(SMC)GASNS LAIRNDEAAPLELRGPNYPNYAMNVGHQGEYAGIAQAAHSARGDAFALNPLVKVAFADPMLVFDFSKPRKEIARGALREF EAAGERDVILPAK A0A2L1CBB0 2.8.4.1 Methanogenesis marker protein 17 Methanococcus maripaludis 0.021119539

Methanogenesis marker protein 17

1 LEVO MAYIDVECNDEAGKAIYERIIQTSLEDLVLGKSIIKAKMICKQDVPYFIIGILPKSTSKLIRLRDIATIDESKKSDGKTI TKLNIDDETYATELLAKINVMDQPSRFEVVTDSEVDLNMVIHDAKEDFIDRVLDFMNRVFPEGMRIRKTIRDKTIVMVAS EKPIEEEWMNEAVKLQEELKIFK G0H411 Methanogenesis marker protein 7 Methanococcus maripaludis 0.035024745999999995

Methanogenesis marker protein

1 LEVO MYQIIRYEGGVYKNNILKEWIEDVGGFIIQEHVMQLDVYMTIAIPQNEIENFKEEAKKYKGKIVETPLAGIEIAIVSPSL SRHHLPHIACDVSEYVRKFGAKPNMIGLAHGAGKNISEIREKEKRLIQEHDIAIYVMGNFESCILDKTHLFKVDIPLVVT GGPETLDIPYTYVGNLGRRAQRLRKGEEIRALRQMIDEVTKKINDKRMELSYDPPIIPPVVLKDEIEKRIDEVRGILAPM PIVTQLDGLRIKMDYDRNHEEIENVKIGKYLLKDIAYVTRSEMKNYILIKLKSTSELKTDENKA Q6M050 Methyl-coenzyme M reductase operon protein C Methanococcus maripaludis 0.024906715

Methyl-coenzyme M reductase subunit C

1 Methanococcus maripaludis LEVO MSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKSAGSGMPVGRKEQIVDCRAVMGLGEGGGLAQRGTFAEGLRNDVVVVAMS PGRRHITKPVCEITYGIREAGIQTSVLVLDAGGGIPSDAPQGSLGSTFGLKPEEAKQVNRHKLCVIHFGNVKSHIIYKAR LFLKYVDIPTIIVCQTPVDMEDFAAIGIKTKNVMPLESKTEGKIVEIITGVIRGESAPQKKIDEIIESIKKHLG G0H3B1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA Methanococcus maripaludis 0.059572561999999996

Methyl-coenzyme M reductase system component A2

1 LEVO MLLLEVKNVSKSYGDTEVLKNVSFELNEGDVMGVLGRSGAGKSVLLHMLRGMEGYEPTSGQIIYHVAYCPHCENVEAPSQ VGKKCECETEYVAKSVDFWNNNEITYALKKKIAIMLQRTFALYGEKTVAENIMEALTAAGYEGKDATEWALNLIKMVKLE HRVAHISRDLSGGEKQRVVLARQIAKNPVIFLADEPTGTLDPKTAKFVHNALTEAVIKHNIAMVITSHWPEVIEELCQKA IWLDKGEMRLVGESKHVVEEFMKTVTSMKEFEKVEVKDELLKLENVEKRYVSVDRGIVKAVDGIDVSINEKEIFGLVGVS GAGKTTLSKIIAAVIPPSKGNYEFRLADEWVDMTKVGPLYRGRAKRYIGMLFQEYSLYPHRTILYNLTESIGLEMPGEFA KMKAEHTLVSVGFTEEEAENMLEKHPSELSVGEKHRVALAQVLIREPHLILLDEPTGTMDPITRNQVAESIQKSRSELDQ TYVIVSHDMDFVLNVCDRAALVRGGKIIKTGKPDEIVKILSEEEKDEMIGH A0A2L1C9A1 DUF2098 domain-containing protein Methanococcus maripaludis 0.010640848999999999

DUF2098 domain-containing protein

1 LEVO MTLDRNGKLIEIGSYVRYINTGTHGTVKAIEPKNDEEWVLLENDIYYRPELLELVERRKIEKKESEEELIERITNEDIDL EAAENGCGCSGAG A0A2L1CAX0 FACTOR 430 0.00090658 2 F43 1-THIOETHANESULFONIC ACID 0.000142197 1 COM Coenzyme B 0.000343334 1 TP7 O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE 0.000481499 1 SHT FeFe cofactor 0.0007473559999999999 3 S5Q ZINC ION 6.5409e-05 1 ZN ADENOSINE-5'-TRIPHOSPHATE 0.000507181 2 ATP MAGNESIUM ION 2.4305e-05 2 MG singleParticle threeDArray 1.25 7.6 20.0 C8H18N2O4S HEPES Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE 25

15 mA

ETHANE-PROPANE 100 277 FEI VITROBOT MARK IV

Vitrification setup inside a Coy Lab's Vinyl anaerobic chamber to preserve the protein sample under strict anaerobic conditions (95% N2/ 5% H2).

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 2.0 FEI FALCON IV (4k x 4k) 28171 60.0

Dataset obtained with 25 degree of pretilting to overcome preferred orientation issues

1 944627 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION ModelAngelo and AlphaFold 2.14 FSC 0.143 CUT-OFF cryoSPARC 118247 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD cryoSPARC emd_51767.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.050428126 0.17514826 0.00013806358 0.0038772034 0.57 0.57 0.57 0.0197 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: AlphaFold in silico model AB INITIO MODEL

Rigid body fitting in Chimera and Coot. Real-space refinement iterative rounds in Phenix.

REAL emd_51767_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.280209 0.44390708 0.000136177 0.008209386 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: emd_51767_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.060944885 0.20039351 0.000136177 0.003262955 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: emd_51767_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.17624035 0.32359818 0.00013737017 0.009349739 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: emd_51767_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.04813548 0.17323971 0.00013737017 0.0039276797 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: emd_51767_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.18275335 0.36564356 0.00013586087 0.006725345 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: emd_51767_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.04920046 0.15110005 0.00013586089 0.0029755137 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: emd_51767_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.20133531 0.3643718 0.0001380636 0.008695993 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: emd_51767_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.22870655 0.2911589 0.00016137112 0.030508583 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767:::: emd_51767_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 342.0 342.0 342.0 90.0 90.0 90.0 X Y Z -0.23848571 0.2966964 0.00016113523 0.030503195 0.57 0.57 0.57 AUTHOR ::::EMDATABANK.org::::EMD-51767::::