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- EMDB-19787: Methyl-coenzyme M reductase activation complex binding to the A2 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-19787
TitleMethyl-coenzyme M reductase activation complex binding to the A2 component
Map data
Sample
  • Complex: Methyl-coenzyme M reductase activation complex binding to A2 component
    • Protein or peptide: x 9 types
  • Ligand: x 8 types
KeywordsMethyl-coenzyme M reductase / activation complex / ATPase / Iron-sulfur clusters / OXIDOREDUCTASE
Function / homology
Function and homology information


organic phosphonate catabolic process / coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Methyl coenzyme M reductase system, component A2 / Methyl-coenzyme M reductase, protein C / Uncharacterised conserved protein UCP019164, methanogenesis / Uncharacterised protein family UPF0288, methanogenesis / Uncharacterised conserved protein UCP019464, methanogenesis / Uncharacterised conserved protein UCP037053 / Protein of unknown function DUF2098 / Methyl-coenzyme M reductase, protein C-like / Methyl-coenzyme M reductase operon protein C / Uncharacterized protein conserved in archaea (DUF2098) ...Methyl coenzyme M reductase system, component A2 / Methyl-coenzyme M reductase, protein C / Uncharacterised conserved protein UCP019164, methanogenesis / Uncharacterised protein family UPF0288, methanogenesis / Uncharacterised conserved protein UCP019464, methanogenesis / Uncharacterised conserved protein UCP037053 / Protein of unknown function DUF2098 / Methyl-coenzyme M reductase, protein C-like / Methyl-coenzyme M reductase operon protein C / Uncharacterized protein conserved in archaea (DUF2098) / Uncharacterized protein conserved in archaea (DUF2113) / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold / Methyl-coenzyme M reductase, alpha subunit, C-terminal / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2 / Methyl-coenzyme M reductase alpha subunit, C-terminal domain / Methyl-coenzyme M reductase alpha subunit, N-terminal domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA / DUF2098 domain-containing protein / Methyl-coenzyme M reductase subunit alpha / Methyl-coenzyme M reductase subunit beta / Methyl-coenzyme M reductase subunit gamma / UPF0288 protein MmarC6_0796 / Methanogenesis marker protein 7 / Methyl-coenzyme M reductase operon protein C / Methanogenesis marker protein 17
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsRamirez-Amador F / Paul S / Kumar A / Schuller JM
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101075992European Union
CitationJournal: Nature / Year: 2025
Title: Structure of the ATP-driven methyl-coenzyme M reductase activation complex.
Authors: Fidel Ramírez-Amador / Sophia Paul / Anuj Kumar / Christian Lorent / Sebastian Keller / Stefan Bohn / Thinh Nguyen / Stefano Lometto / Dennis Vlegels / Jörg Kahnt / Darja Deobald / Frank ...Authors: Fidel Ramírez-Amador / Sophia Paul / Anuj Kumar / Christian Lorent / Sebastian Keller / Stefan Bohn / Thinh Nguyen / Stefano Lometto / Dennis Vlegels / Jörg Kahnt / Darja Deobald / Frank Abendroth / Olalla Vázquez / Georg Hochberg / Silvan Scheller / Sven T Stripp / Jan Michael Schuller /
Abstract: Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane. Its active site comprises coenzyme F, a porphyrin-based cofactor with a central nickel ion ...Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane. Its active site comprises coenzyme F, a porphyrin-based cofactor with a central nickel ion that is active exclusively in the Ni(I) state. How methanogenic archaea perform the reductive activation of F represents a major gap in our understanding of one of the most ancient bioenergetic systems in nature. Here we purified and characterized the MCR activation complex from Methanococcus maripaludis. McrC, a small subunit encoded in the mcr operon, co-purifies with the methanogenic marker proteins Mmp7, Mmp17, Mmp3 and the A2 component. We demonstrated that this complex can activate MCR in vitro in a strictly ATP-dependent manner, enabling the formation of methane. In addition, we determined the cryo-electron microscopy structure of the MCR activation complex exhibiting different functional states with local resolutions reaching 1.8-2.1 Å. Our data revealed three complex iron-sulfur clusters that formed an electron transfer pathway towards F. Topology and electron paramagnetic resonance spectroscopy analyses indicate that these clusters are similar to the [8Fe-9S-C] cluster, a maturation intermediate of the catalytic cofactor in nitrogenase. Altogether, our findings offer insights into the activation mechanism of MCR and prospects on the early evolution of nitrogenase.
History
DepositionMar 4, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19787.png

Downloads & links

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Map

FileDownload / File: emd_19787.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 350.4 Å		0.73 Å/pix.
x 480 pix.
= 350.4 Å		0.73 Å/pix.
x 480 pix.
= 350.4 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
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Contour LevelBy AUTHOR: 0.051
Minimum - Maximum-0.20102896 - 0.55211896
Average (Standard dev.)0.00014773836 (±0.011461655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 350.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19787_msk_1.map
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Mask #2

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Mask #3

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Mask #4

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Mask #5

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Half map: #2

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Sample components

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Entire : Methyl-coenzyme M reductase activation complex binding to A2 component

EntireName: Methyl-coenzyme M reductase activation complex binding to A2 component
Components
  • Complex: Methyl-coenzyme M reductase activation complex binding to A2 component
    • Protein or peptide: Methyl-coenzyme M reductase subunit gamma
    • Protein or peptide: Methyl-coenzyme M reductase subunit alpha
    • Protein or peptide: Methyl-coenzyme M reductase subunit beta
    • Protein or peptide: Methanogenesis marker protein 17
    • Protein or peptide: Methanogenesis marker protein 7
    • Protein or peptide: Methyl-coenzyme M reductase operon protein C
    • Protein or peptide: UPF0288 protein MmarC6_0796
    • Protein or peptide: Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA
    • Protein or peptide: DUF2098 domain-containing protein
  • Ligand: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE
  • Ligand: Coenzyme B
  • Ligand: 1-THIOETHANESULFONIC ACID
  • Ligand: FACTOR 430
  • Ligand: FeFe cofactor
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Methyl-coenzyme M reductase activation complex binding to A2 component

SupramoleculeName: Methyl-coenzyme M reductase activation complex binding to A2 component
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2, #4-#6, #8, #7, #9
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: Methyl-coenzyme M reductase subunit gamma

MacromoleculeName: Methyl-coenzyme M reductase subunit gamma / type: protein_or_peptide / ID: 1 / Details: Methyl-coenzyme M reductase subunit gamma / Number of copies: 2 / Enantiomer: LEVO / EC number: coenzyme-B sulfoethylthiotransferase
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 29.665488 KDa
SequenceString: MAYTPQFYPG ATKVAENRRN HLNPNYELEK LREIPDEDVV KIMGHRQPGE DYKTVHPPLE EMDFVEDYAR DLVEPLNGAK EGHRVRYIQ FADSMYFAPA QPYDRSRSYM SRLRGVDAGT LSGRQVVECR ESDLEEFSKN ILMDTELFDP ATSGMRGATV H GHSLRLDE ...String:
MAYTPQFYPG ATKVAENRRN HLNPNYELEK LREIPDEDVV KIMGHRQPGE DYKTVHPPLE EMDFVEDYAR DLVEPLNGAK EGHRVRYIQ FADSMYFAPA QPYDRSRSYM SRLRGVDAGT LSGRQVVECR ESDLEEFSKN ILMDTELFDP ATSGMRGATV H GHSLRLDE NGMMFDALQR CVFDEKTGHV MYVKDQVGKP LDAPVDVGEP IPEAKLREIT TIYRNDGVAM RADPDVIEVV KR IHRARTL GGYIPTNETF KGL

UniProtKB: Methyl-coenzyme M reductase subunit gamma

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Macromolecule #2: Methyl-coenzyme M reductase subunit beta

MacromoleculeName: Methyl-coenzyme M reductase subunit beta / type: protein_or_peptide / ID: 2 / Details: Methyl-coenzyme M reductase subunit beta / Number of copies: 2 / Enantiomer: LEVO / EC number: coenzyme-B sulfoethylthiotransferase
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 46.701203 KDa
SequenceString: MVKYEDKISL YDAKGNLVAE NVPLEAISPL YNPTIKSMVK NIKRTVAVNL AGIEGTLAAG KIGGKGCQVP GRTLDISAVS NAQAIADEV EKILKVSEDD DTAVKIINGG KQLAVQVPTA RLEVAAEYSV SMLSTAMALK EALIKTFNID MFDGSTVHAA I VGNYPQVM ...String:
MVKYEDKISL YDAKGNLVAE NVPLEAISPL YNPTIKSMVK NIKRTVAVNL AGIEGTLAAG KIGGKGCQVP GRTLDISAVS NAQAIADEV EKILKVSEDD DTAVKIINGG KQLAVQVPTA RLEVAAEYSV SMLSTAMALK EALIKTFNID MFDGSTVHAA I VGNYPQVM DYAGGNIASL LGAPSMMEGL GYALRNIPVN HAVATTKKNM MNAIAFSSVM EQTATFEMGD AVGSFERQHL LG LAYQGLN ADNLVIDFIK ANAKGTVGSV VETVIDRAIA DGVIVVDKTM SSGFNMYKPA DVNKWNAYAA AGLVAAVAVS CGA ARAAQN VASVILYFND ILEYETGLPG VDYGRSMGTA VGFSFFSHSI YGGGGPGIFN GNHVVTRHSK GFAIPPVCAA MCAD AGTQM FSPEHTSGLV GSVYSAFDEF REPMKYVIEG ALSIKDQF

UniProtKB: Methyl-coenzyme M reductase subunit beta

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Macromolecule #3: Methyl-coenzyme M reductase subunit alpha

MacromoleculeName: Methyl-coenzyme M reductase subunit alpha / type: protein_or_peptide / ID: 3 / Details: Methyl-coenzyme M reductase subunit alpha / Number of copies: 2 / Enantiomer: LEVO / EC number: coenzyme-B sulfoethylthiotransferase
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 61.230703 KDa
SequenceString: MEAEKRLFLK ALKEKFEEDP KEKYTKFYTF GGWEQSARKR EFVEANEKIV SEKRQGIPLY NPDIGVPLGQ RKLMPYKLSN TDDYCEGDD LHFLNNAAIQ QLWDDIRRTV IVGMDTAHSV LEKRLGVEVT PETINEYMHT INHSLPGGAV VQEHMVEVHP S LAWDCYAR ...String:
MEAEKRLFLK ALKEKFEEDP KEKYTKFYTF GGWEQSARKR EFVEANEKIV SEKRQGIPLY NPDIGVPLGQ RKLMPYKLSN TDDYCEGDD LHFLNNAAIQ QLWDDIRRTV IVGMDTAHSV LEKRLGVEVT PETINEYMHT INHSLPGGAV VQEHMVEVHP S LAWDCYAR IFTGDDELAD ELDSRFLIDI NKLFPEEQAE TLKAAIGKKT YQVSRVPSLV GRVCDGGTIS RWSAMQIGMS FI TAYKLCA GEAATADFSY ASK(MHS)ADVIQM GNALPGR(AGM)AR GPNEPGGIRF GILSDVVQTT RVSEDPVEQS LEVVA TGAA LYDQIWLGAY MSGGIGFTQY ATASYTDDIL DDFSYYALDY VEKKYGRMGT KATMDVVEDV AGEVTLYALE QYDDYP ALL EDHFGGS(MGN)RA AVAAAASGIG VCMATGNSNA GVNGWYLSQI LHKEYHSRLG FY(GL3)YDLQDQ(SMC) GASNS LAIR NDEAAPLELR GPNYPNYAMN VGHQGEYAGI AQAAHSARGD AFALNPLVKV AFADPMLVFD FSKPRKEIAR GALREF EAA GERDVILPAK

UniProtKB: Methyl-coenzyme M reductase subunit alpha

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Macromolecule #4: Methanogenesis marker protein 17

MacromoleculeName: Methanogenesis marker protein 17 / type: protein_or_peptide / ID: 4 / Details: Methanogenesis marker protein 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 21.119539 KDa
SequenceString:
MAYIDVECND EAGKAIYERI IQTSLEDLVL GKSIIKAKMI CKQDVPYFII GILPKSTSKL IRLRDIATID ESKKSDGKTI TKLNIDDET YATELLAKIN VMDQPSRFEV VTDSEVDLNM VIHDAKEDFI DRVLDFMNRV FPEGMRIRKT IRDKTIVMVA S EKPIEEEW MNEAVKLQEE LKIFK

UniProtKB: Methanogenesis marker protein 17

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Macromolecule #5: Methanogenesis marker protein 7

MacromoleculeName: Methanogenesis marker protein 7 / type: protein_or_peptide / ID: 5 / Details: Methanogenesis marker protein 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 35.024746 KDa
SequenceString: MYQIIRYEGG VYKNNILKEW IEDVGGFIIQ EHVMQLDVYM TIAIPQNEIE NFKEEAKKYK GKIVETPLAG IEIAIVSPSL SRHHLPHIA CDVSEYVRKF GAKPNMIGLA HGAGKNISEI REKEKRLIQE HDIAIYVMGN FESCILDKTH LFKVDIPLVV T GGPETLDI ...String:
MYQIIRYEGG VYKNNILKEW IEDVGGFIIQ EHVMQLDVYM TIAIPQNEIE NFKEEAKKYK GKIVETPLAG IEIAIVSPSL SRHHLPHIA CDVSEYVRKF GAKPNMIGLA HGAGKNISEI REKEKRLIQE HDIAIYVMGN FESCILDKTH LFKVDIPLVV T GGPETLDI PYTYVGNLGR RAQRLRKGEE IRALRQMIDE VTKKINDKRM ELSYDPPIIP PVVLKDEIEK RIDEVRGILA PM PIVTQLD GLRIKMDYDR NHEEIENVKI GKYLLKDIAY VTRSEMKNYI LIKLKSTSEL KTDENKA

UniProtKB: Methanogenesis marker protein 7

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Macromolecule #6: Methyl-coenzyme M reductase operon protein C

MacromoleculeName: Methyl-coenzyme M reductase operon protein C / type: protein_or_peptide / ID: 6 / Details: Methyl-coenzyme M reductase operon protein C / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 24.906715 KDa
Recombinant expressionOrganism: Methanococcus maripaludis (archaea)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSAGSGMPVG RKEQIVDCRA VMGLGEGGGL AQRGTFAEGL RNDVVVVAMS PGRRHITKP VCEITYGIRE AGIQTSVLVL DAGGGIPSDA PQGSLGSTFG LKPEEAKQVN RHKLCVIHFG NVKSHIIYKA R LFLKYVDI ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSAGSGMPVG RKEQIVDCRA VMGLGEGGGL AQRGTFAEGL RNDVVVVAMS PGRRHITKP VCEITYGIRE AGIQTSVLVL DAGGGIPSDA PQGSLGSTFG LKPEEAKQVN RHKLCVIHFG NVKSHIIYKA R LFLKYVDI PTIIVCQTPV DMEDFAAIGI KTKNVMPLES KTEGKIVEII TGVIRGESAP QKKIDEIIES IKKHLG

UniProtKB: Methyl-coenzyme M reductase operon protein C

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Macromolecule #7: Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA

MacromoleculeName: Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA
type: protein_or_peptide / ID: 7 / Details: Methyl-coenzyme M reductase system, component A2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 59.572562 KDa
SequenceString: MLLLEVKNVS KSYGDTEVLK NVSFELNEGD VMGVLGRSGA GKSVLLHMLR GMEGYEPTSG QIIYHVAYCP HCENVEAPSQ VGKKCECET EYVAKSVDFW NNNEITYALK KKIAIMLQRT FALYGEKTVA ENIMEALTAA GYEGKDATEW ALNLIKMVKL E HRVAHISR ...String:
MLLLEVKNVS KSYGDTEVLK NVSFELNEGD VMGVLGRSGA GKSVLLHMLR GMEGYEPTSG QIIYHVAYCP HCENVEAPSQ VGKKCECET EYVAKSVDFW NNNEITYALK KKIAIMLQRT FALYGEKTVA ENIMEALTAA GYEGKDATEW ALNLIKMVKL E HRVAHISR DLSGGEKQRV VLARQIAKNP VIFLADEPTG TLDPKTAKFV HNALTEAVIK HNIAMVITSH WPEVIEELCQ KA IWLDKGE MRLVGESKHV VEEFMKTVTS MKEFEKVEVK DELLKLENVE KRYVSVDRGI VKAVDGIDVS INEKEIFGLV GVS GAGKTT LSKIIAAVIP PSKGNYEFRL ADEWVDMTKV GPLYRGRAKR YIGMLFQEYS LYPHRTILYN LTESIGLEMP GEFA KMKAE HTLVSVGFTE EEAENMLEKH PSELSVGEKH RVALAQVLIR EPHLILLDEP TGTMDPITRN QVAESIQKSR SELDQ TYVI VSHDMDFVLN VCDRAALVRG GKIIKTGKPD EIVKILSEEE KDEMIGH

UniProtKB: Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA

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Macromolecule #8: UPF0288 protein MmarC6_0796

MacromoleculeName: UPF0288 protein MmarC6_0796 / type: protein_or_peptide / ID: 8 / Details: Methanogenesis marker protein 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 56.520801 KDa
SequenceString: MNVLVNNNPK SGKTLEDVIK DEYYIPGSNI VIIKGTATVI KEETKKYLIK TTKGSFVVGI TEENETVDFW NKNYKSFEDK SLIWKSISD VSFGSIEIPL PVSSVKQNFK KWDVVLSVSG LDTSEGNLIF VQRDVLELYG LENPKIGILI GGKRVLKTLT A DDRIISIE ...String:
MNVLVNNNPK SGKTLEDVIK DEYYIPGSNI VIIKGTATVI KEETKKYLIK TTKGSFVVGI TEENETVDFW NKNYKSFEDK SLIWKSISD VSFGSIEIPL PVSSVKQNFK KWDVVLSVSG LDTSEGNLIF VQRDVLELYG LENPKIGILI GGKRVLKTLT A DDRIISIE QMRESKENID YEITTNLNKE IQDTWKIYTY CKAEFDGPPQ STEHALAILE NGTLEISENT NTYVADCRLQ TL FIDEENP EDRDRGTITV RNIGNGVGKV YIYQESRASS LSHTVVGKVT DGIEIVDFSN SGHITVKTNP ERLSVIGKTQ KDA KILFEK HGITLKMEGN IDEDAIIVEQ VPEYTMDILK SKEVTTKGIE PEKLLYVEIY DKDAPTTSWY FRKVTGLTTK RIGT LKIYF KHDDISMFER DWDYSKGLLP ENTPEKSIDS GIIAVTNMVK KYKGYIGVRT SSNDKYGPTG ETFEGTNIVG KVVKN SEIL KSVKQGENIY ILEVNSN

UniProtKB: UPF0288 protein MmarC6_0796

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Macromolecule #9: DUF2098 domain-containing protein

MacromoleculeName: DUF2098 domain-containing protein / type: protein_or_peptide / ID: 9 / Details: DUF2098 domain-containing protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 10.640849 KDa
SequenceString:
MTLDRNGKLI EIGSYVRYIN TGTHGTVKAI EPKNDEEWVL LENDIYYRPE LLELVERRKI EKKESEEELI ERITNEDIDL EAAENGCGC SGAG

UniProtKB: DUF2098 domain-containing protein

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Macromolecule #10: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE

MacromoleculeName: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE
type: ligand / ID: 10 / Number of copies: 1 / Formula: SHT
Molecular weightTheoretical: 481.499 Da
Chemical component information

ChemComp-SHT:
O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE

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Macromolecule #11: Coenzyme B

MacromoleculeName: Coenzyme B / type: ligand / ID: 11 / Number of copies: 1 / Formula: TP7
Molecular weightTheoretical: 343.334 Da
Chemical component information

ChemComp-TP7:
Coenzyme B

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Macromolecule #12: 1-THIOETHANESULFONIC ACID

MacromoleculeName: 1-THIOETHANESULFONIC ACID / type: ligand / ID: 12 / Number of copies: 1 / Formula: COM
Molecular weightTheoretical: 142.197 Da
Chemical component information

ChemComp-COM:
1-THIOETHANESULFONIC ACID

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Macromolecule #13: FACTOR 430

MacromoleculeName: FACTOR 430 / type: ligand / ID: 13 / Number of copies: 2 / Formula: F43
Molecular weightTheoretical: 906.58 Da
Chemical component information

ChemComp-F43:
FACTOR 430

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Macromolecule #14: FeFe cofactor

MacromoleculeName: FeFe cofactor / type: ligand / ID: 14 / Number of copies: 3 / Formula: S5Q
Molecular weightTheoretical: 747.356 Da
Chemical component information

ChemComp-S5Q:
FeFe cofactor

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Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #16: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 16 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration1.25 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification setup inside a Coy Lab's Vinyl Anaerobic Chamber to preserve the protein sample under strict anaerobic conditions (95% O2 / 5% H2)..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 17548 / Average electron dose: 60.0 e/Å2
Details: 7781 micrographs with a 20 deg pretilt to overcome preferred orientation problems
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1557902
Details: 1023667 from non tilted and 534235 from pretilted datasets
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ModelAngelo and AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 484016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC
Details: 2D classification for the global map reconstruction and 3D classification on the masking-local refinement steps for particular regions
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsRigid body fitting in Chimera and Coot. Further real-space refinement in Phenix.
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8s7v:
Methyl-coenzyme M reductase activation complex binding to the A2 component

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