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- EMDB-55299: Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marbu... -

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Basic information

Entry
Database: EMDB / ID: EMD-55299
TitleStructure of the Mvh-Hdr-Fmd complex of Methanothermobacter marburgensis (composite structure)
Map dataComposite map of the Mvh-Hdr-Fmd complex
Sample
  • Complex: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis
    • Protein or peptide: x 12 types
  • Ligand: x 12 types
KeywordsOxidoreductase / hydrogenase / dehydrogenase / polyferredoxin
Function / homology
Function and homology information


formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / methanogenesis, from carbon dioxide / CoB--CoM heterodisulfide reductase activity / methanogenesis / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdenum ion binding ...formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / methanogenesis, from carbon dioxide / CoB--CoM heterodisulfide reductase activity / methanogenesis / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdenum ion binding / ferredoxin hydrogenase activity / molybdopterin cofactor binding / nickel cation binding / NADH dehydrogenase activity / iron-sulfur cluster binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / iron ion binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Formylmethanofuran dehydrogenase, fused subunit C/D / 4Fe-4S binding domain / FwdD/FmdC, molybdopterin dinucleotide-binding domain / : / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / : ...Formylmethanofuran dehydrogenase, fused subunit C/D / 4Fe-4S binding domain / FwdD/FmdC, molybdopterin dinucleotide-binding domain / : / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / : / 3Fe-4S ferredoxin / Glutamate synthase, alpha subunit, C-terminal domain superfamily / : / MnmG, N-terminal domain / Glucose inhibited division protein A / CoB--CoM heterodisulphide reductase, subunit B / : / CoB--CoM heterodisulphide reductase, subunit C / Cysteine-rich domain / Amidohydrolase 3 / Cysteine-rich domain / Amidohydrolase family / F420-non-reducing hydrogenase iron-sulfur subunit D / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / : / 4Fe-4S dicluster domain / : / HoxL-like / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Alpha-helical ferredoxin / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Metal-dependent hydrolase, composite domain superfamily / FAD/NAD(P)-binding domain / Aspartate decarboxylase-like domain superfamily / Pyridine nucleotide-disulphide oxidoreductase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / Metal-dependent hydrolase / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Tungsten formylmethanofuran dehydrogenase, subunit F / Tungsten formylmethanofuran dehydrogenase, subunit G / Tungsten formylmethanofuran dehydrogenase, subunit A / formylmethanofuran dehydrogenase subunit B / F420-non-reducing hydrogenase subunit A / Polyferredoxin protein MvhB / F420-non-reducing hydrogenase iron-sulfur subunit D / F420-non-reducing hydrogenase subunit G / Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C ...Tungsten formylmethanofuran dehydrogenase, subunit F / Tungsten formylmethanofuran dehydrogenase, subunit G / Tungsten formylmethanofuran dehydrogenase, subunit A / formylmethanofuran dehydrogenase subunit B / F420-non-reducing hydrogenase subunit A / Polyferredoxin protein MvhB / F420-non-reducing hydrogenase iron-sulfur subunit D / F420-non-reducing hydrogenase subunit G / Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSan Segundo-Acosta P / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Sci Adv / Year: 2026
Title: Diversity of electron-bifurcating CO-fixing supercomplexes in methanogens.
Authors: Pablo San Segundo-Acosta / Shunsuke Nomura / Joao Pedro Fernandes-Queiroz / Evgenii Protasov / Jörg Kahnt / Masanori Kaneko / Georg Hochberg / Seigo Shima / Bonnie J Murphy /
Abstract: In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) reduces and fixes CO, driven by low-potential electrons provided by electron-bifurcating heterodisulfide reductase ...In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) reduces and fixes CO, driven by low-potential electrons provided by electron-bifurcating heterodisulfide reductase (Hdr) complexed with electron-donating proteins such as Mvh hydrogenase. Here, we report the structure of a C2-symmetric (Mvh-Hdr)-Fmd supercomplex from a Class I methanogen, , which is architecturally different from the previously reported ring-shaped D3-symmetric supercomplex of a methanogen belonging to phylogenetically distinct Class II methanogens. In this C2-symmetric form, the redox active sites of Hdr and Fmd are connected by two MvhB polyferredoxins, whose branching electron paths appear to be available for electron transfer to/from other partners. The ancestral form was likely C2 symmetric, whereas D3-symmetric supercomplexes were acquired by horizontal gene transfer, a transition probably helpful for growth in substrate-poor environments.
History
DepositionOct 4, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55299.png

Downloads & links

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Map

FileDownload / File: emd_55299.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the Mvh-Hdr-Fmd complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 401.1 Å		0.84 Å/pix.
x 480 pix.
= 401.1 Å		0.84 Å/pix.
x 480 pix.
= 401.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83563 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.2
Minimum - Maximum-28.133669999999999 - 50.92418
Average (Standard dev.)0.012208479 (±0.9164779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 401.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzym...

EntireName: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis
Components
  • Complex: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
    • Protein or peptide: F420-non-reducing hydrogenase iron-sulfur subunit D
    • Protein or peptide: F420-non-reducing hydrogenase subunit G
    • Protein or peptide: Tungsten formylmethanofuran dehydrogenase, subunit F
    • Protein or peptide: Tungsten formylmethanofuran dehydrogenase, subunit A
    • Protein or peptide: formylmethanofuran dehydrogenase subunit B
    • Protein or peptide: Tungsten formylmethanofuran dehydrogenase, subunit G
    • Protein or peptide: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
    • Protein or peptide: Polyferredoxin protein MvhB
    • Protein or peptide: F420-non-reducing hydrogenase subunit A
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: ZINC ION
  • Ligand: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
  • Ligand: MOLYBDENUM ATOM
  • Ligand: HYDROSULFURIC ACID
  • Ligand: FE3-S4 CLUSTER
  • Ligand: CARBONMONOXIDE-(DICYANO) IRON
  • Ligand: NICKEL (II) ION
  • Ligand: water

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Supramolecule #1: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzym...

SupramoleculeName: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 72.264961 KDa
SequenceString: MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFR RCVEEAGLNQ FLFEFANIRE HDSWVHMDNP EGATEKAKDL VRMAVAKARL LEPLEASKVS VDDKALVIGG G VAGIQAAL ...String:
MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFR RCVEEAGLNQ FLFEFANIRE HDSWVHMDNP EGATEKAKDL VRMAVAKARL LEPLEASKVS VDDKALVIGG G VAGIQAAL DLADMGFKTY MVEKRPSISG RMGQLDKTFP TLDCSMCILA PKMVDVGKHD NIELITYAEV KEVDGYIGNF KV KIEKKPR YIDEELCTGC GSCVEVCPIE MPNYFDEGIG MTKAVYIPFP QAVPLCATID KDYCIECMLC DEVCERGAVK HDQ EPEEIE IEVGTIIVAT GYDAYDPTEK LEYGYGRHTN VITGLELERM INASGPTDGK VLKPSDGEKP KRVAFIHCVG SRDE QIGKP YCSRVCCMYI MKNAQLIKDK MPDTEVTLYY MDIRAFGKGF EEFYKRSQEK YGIKFIRGRP AEVIENPDLT LTVRS EDTL LGKVTEYDYD MVVLGVGLVP PEGAETLRQT IGLSKSADGF LMEAHPKLRP VDTLTDGVYL AGVAQGPKDI PDAVAQ ASG AAARAAIPMV KGEVEIEPII AVTDSDVCGG CEVCIELCPF GAISIEEGHA NVNVALCKGC GTCVAACPSG AMDQQHF KT EQIMAQIEAA LNEPASK

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

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Macromolecule #2: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 33.496371 KDa
SequenceString: MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE ...String:
MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE RPTILDEIVE VTGAKSVEYK DKMMCCGAGG GVRSRDLDVA LDFTREKLTN MKEAGVDAIV NVCPFCHLQF DV GQMEIKD KFGEEFDIPV LHLAQLLGLA MGLPKEDLVV DAHQVCVDEC LEKLEELDRL APGSG

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

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Macromolecule #3: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 20.548727 KDa
SequenceString:
MTLLQREENI IRKGNIDKEF SEKIKAAGGD SLEYCFQCGT CTGSCPSGRR TPYRVRQIIR KANVGLKDEI ISDPTLWMCT TCYSCQERC PRKVKIVDVV KLARNEAAKA GFMAPAHKAV GSFVIKTGHG VPINDATMEL RKAVGLGELP PTTHQFPEAL E EVQKIIKA TGFDQLIGYN WETGELE

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

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Macromolecule #4: F420-non-reducing hydrogenase iron-sulfur subunit D

MacromoleculeName: F420-non-reducing hydrogenase iron-sulfur subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 15.954442 KDa
SequenceString:
MAEDDIKIVM FCCNWCSYGG ADTAGTARMQ YPTNIRVIRV MCSGRIEPQF VFKAFREGAD GVLVTGCHHG DCHYDAGNYK LDRRMRLIY KLADELGIGR ERIHHDWISA SEGEKFAETV KMMVDRIRAL GPSPIKKQLA EA

UniProtKB: F420-non-reducing hydrogenase iron-sulfur subunit D

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Macromolecule #5: F420-non-reducing hydrogenase subunit G

MacromoleculeName: F420-non-reducing hydrogenase subunit G / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 33.786582 KDa
SequenceString: MAEKIKIGTM WLGGCSGCHL SIADFHEKLL DVMEHADFEF SPVLMDTKYD EIPELDVVVI EGGIVNDENR EFAEELREKA KFVISYGTC AVYGGIPGLR NLWDKDEVIE EAYINSITTP NEEGVIPSED VPHLEGRVKP LGEVIDVDFE VPGCPPRSDV A AEVVMALL ...String:
MAEKIKIGTM WLGGCSGCHL SIADFHEKLL DVMEHADFEF SPVLMDTKYD EIPELDVVVI EGGIVNDENR EFAEELREKA KFVISYGTC AVYGGIPGLR NLWDKDEVIE EAYINSITTP NEEGVIPSED VPHLEGRVKP LGEVIDVDFE VPGCPPRSDV A AEVVMALL KGEEIELPST NLCEVCPREK PPEGLAMDFI KRQFEVGKPE DDLCLIPQGL ICMGPATVSI CGAECPSIAI PC RGCYGPT ARVEDQGAKM ISAIASDYKV EEDKTVDPEE VAEQLDDIVG TFYTFTLPAA LIPMKIKKEG K

UniProtKB: F420-non-reducing hydrogenase subunit G

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Macromolecule #6: Tungsten formylmethanofuran dehydrogenase, subunit F

MacromoleculeName: Tungsten formylmethanofuran dehydrogenase, subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 38.614516 KDa
SequenceString: METTEVIEGK NITVERTGEE NRKLIFQDCL CAVCGLCGEI CPVSAIEVNP TGAMVRTEQD ESKILIDENK CVLCGMCSSI CPFQALDLQ IDGTSIKELA EYPKILKSAE IDDETCIQCK ACETACPQDA ITITRELPER KDLITGEIEI DKDTCIYCGM C EEMCPVDA ...String:
METTEVIEGK NITVERTGEE NRKLIFQDCL CAVCGLCGEI CPVSAIEVNP TGAMVRTEQD ESKILIDENK CVLCGMCSSI CPFQALDLQ IDGTSIKELA EYPKILKSAE IDDETCIQCK ACETACPQDA ITITRELPER KDLITGEIEI DKDTCIYCGM C EEMCPVDA IEIEHQIPSS SSPTVATDIN VDEDKCVHCG ICKRICPVDA IMQVCRICPY GEYEIKVPEV TGTSYIDPEL CV NCGWCQE ICPVDAATVT KPFEGELIID QDTCQACETC VMACPCNVLS FPKPEKSGEK PTKLYKDERF CIYCGACERS CPV NAIEVK RSRINTTPIK SKAWKNAFES LLK

UniProtKB: Tungsten formylmethanofuran dehydrogenase, subunit F

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Macromolecule #7: Tungsten formylmethanofuran dehydrogenase, subunit A

MacromoleculeName: Tungsten formylmethanofuran dehydrogenase, subunit A / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 63.00182 KDa
SequenceString: MEYIIKNGFV YCPLNNVDGE KMDICVRDGK IVESVSDSAK VIDASGKIVM PGGVDPHSHI AGAKVNVGRM YRPEDSRRDA EKFKAGRAG SGFSVPSTFM TGYRYAQMGY TTAMEAAMPP LLARHTHEEF HDTPIIDHAA YPLFGNNWFV MEYLKEGDVD A CAAYASWL ...String:
MEYIIKNGFV YCPLNNVDGE KMDICVRDGK IVESVSDSAK VIDASGKIVM PGGVDPHSHI AGAKVNVGRM YRPEDSRRDA EKFKAGRAG SGFSVPSTFM TGYRYAQMGY TTAMEAAMPP LLARHTHEEF HDTPIIDHAA YPLFGNNWFV MEYLKEGDVD A CAAYASWL LKATKGYTI(KCX) IVNPAGTEAW GWGGNVHGIH DPAPYFDITP AEIIKGLAEV NEKLQLPHSI HLHCNDLG H PGNYETTLAS FDVPKNIKAN PATGERDTVL YATHVQFHSY GGTTWRDFVS EAPKIADYVN KNDHIVIDVG QITLDETTT MTADGPMEYD LHSLNGLKWA NCDVELETGS GVVPFIYSAR APVPAVQWAI GMELFLLIDD PAKVCLTTDS PNAGPFTRYP RVIAWLMSN KYRMNLIEGE LHKWAQRKST IATVDREYTF SEIAQITRST SAKVLGLSET KGHLGVGADA DIAVYNINPE T VDPSVDYM AIEEGFSRAA YVLKDGEIVV KDGEVVASPH GRTYWVDTRV DESTYNEVLA KVESKFKQYY SVNFANYPVQ DE YLPKSAP VKGVML

UniProtKB: Tungsten formylmethanofuran dehydrogenase, subunit A

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Macromolecule #8: formylmethanofuran dehydrogenase subunit B

MacromoleculeName: formylmethanofuran dehydrogenase subunit B / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 48.179773 KDa
SequenceString: MSVYKNVTCP VCGGSCDDIE VLYDGKTIKT RNACRMGNAK FQEMVSSHRI LRPQIKTESG FRSAEWDEAL DAAAEILTES KRPTLFMGS EMSTEAMAAG LELGEYLNAM VDSNATICHG PTLMGIQEAG QSAATAGEIK NRADVIIYWG TNVMDSMPRH M SRYSIFMR ...String:
MSVYKNVTCP VCGGSCDDIE VLYDGKTIKT RNACRMGNAK FQEMVSSHRI LRPQIKTESG FRSAEWDEAL DAAAEILTES KRPTLFMGS EMSTEAMAAG LELGEYLNAM VDSNATICHG PTLMGIQEAG QSAATAGEIK NRADVIIYWG TNVMDSMPRH M SRYSIFMR GFFRERGKKD RTVISVDPRE TATTKASDIH LQLKPNSDYE LFSALLTVIR GNEPHRSIES ITGISVETIK EV ADIMLNA QFGAIYGGLG LASSEGKHRN VEMVLKLVAA LNEHTKFTIG AIRGHCNVAG FNQVASWEYG FPFGVDFTRG YPR YNPGET TIVDLLQRKE SDAVLVICSD LGAHLPKECV EYMKEIPVIC IDIAPCPTTL VSDVVIPGVI DAMESSGTFY RFDN VPIHH KAFTTSPFPE TESNEHTLRQ ILERVKSIKG E

UniProtKB: formylmethanofuran dehydrogenase subunit B

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Macromolecule #9: Tungsten formylmethanofuran dehydrogenase, subunit G

MacromoleculeName: Tungsten formylmethanofuran dehydrogenase, subunit G / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 8.564948 KDa
SequenceString:
MAIGLKAYPE LCHGCGNCVI ACPVNALRSP EVAGGKGPTD DVEIIMIVED GVVNIKNPDL CGKCGTCVES CPVDAIRLEE LE

UniProtKB: Tungsten formylmethanofuran dehydrogenase, subunit G

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Macromolecule #10: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C

MacromoleculeName: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 43.383215 KDa
SequenceString: MGFVLVPKSD FQIPLEADTI RPDLFEGLDL DEIRSLQVYE GNIKRPLGEF FEIAETSHED QLIRIDGDVS RVKYIGSGMK SGKIIINGD VGLQLGCEMK GGEIEVNGNV SSWIGMEMHG GTIKINGNAG DYVGCAYRGE WRGMKGGKII IQGNAGNNIG G GMMAGEIY ...String:
MGFVLVPKSD FQIPLEADTI RPDLFEGLDL DEIRSLQVYE GNIKRPLGEF FEIAETSHED QLIRIDGDVS RVKYIGSGMK SGKIIINGD VGLQLGCEMK GGEIEVNGNV SSWIGMEMHG GTIKINGNAG DYVGCAYRGE WRGMKGGKII IQGNAGNNIG G GMMAGEIY IGGDAGNFCG IRMNGGEITV RGDAGRAPGA EMVSGIIKIH GRISSLLPGF KEISTFKEDG SLMILFKGDL SE KNPEGNL YINYNKNLHI LENETDEGRV ITKKGIKVIY NSGSTIREGQ IIKGGNKLTD DYIDECARCC ISPEDYKLLG EPE NVVVSS HGNEVVLRAV EDPGIQMGTI FIPRGIWANV LTPPYTESTG SPMYKGVPVY LRKASQGERI LSAEELVEEY GVGK

UniProtKB: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C

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Macromolecule #11: Polyferredoxin protein MvhB

MacromoleculeName: Polyferredoxin protein MvhB / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 44.09043 KDa
SequenceString: MIVVNKEDCI RCGACQGTCP TAAIEVTPED VIYCDICGGE PKCVDACPTG ALKIEDLVVD EAGNTQGRIV FNPDKCNECG DCVEVCPPQ ILKLDEGKVK KIPLQGFCVM CQKCVDICPV GVIGVEGIKE PAKVELEIEG PIFIADCVGC GMCVPECPVD A ITLEKVGG ...String:
MIVVNKEDCI RCGACQGTCP TAAIEVTPED VIYCDICGGE PKCVDACPTG ALKIEDLVVD EAGNTQGRIV FNPDKCNECG DCVEVCPPQ ILKLDEGKVK KIPLQGFCVM CQKCVDICPV GVIGVEGIKE PAKVELEIEG PIFIADCVGC GMCVPECPVD A ITLEKVGG VIEIDEDTCI KCGVCAQTCP WNAVYISGKK PEKRAKEIRK FELDEEACIG CNTCVEACPG DFIVPKSSNL TV ELPAICT ACGLCEQLCP VDAIDLDVEL GPAKPASEEG LVWDEGKCDF IGACANICPN DAIRVVTREG MKLPDNEKVD EEP SFAMCT RCGACTMACP KGALSLVDMD KVIDGEVVKR KRVQYNPALC DQCGDCIEAC PYDMLKLTDE KVPLKGFCIL CDQC IPACP KGALSLK

UniProtKB: Polyferredoxin protein MvhB

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Macromolecule #12: F420-non-reducing hydrogenase subunit A

MacromoleculeName: F420-non-reducing hydrogenase subunit A / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 52.905051 KDa
SequenceString: MVKLTMEPVT RIEGHAKITV HLDDAGNVED TRLHVMEFRG FEKFLQGRPI EEAPRIVPRI CGICDVQHHL AAAKAVDACF GFEPDDVLP AAYKMREIMN WGSYMHSHGL HFYFLAAPDF IAGKDRKTRN VFQIIKDAPD VALQAIELRK NALEIVRATG G RPIHPTSS ...String:
MVKLTMEPVT RIEGHAKITV HLDDAGNVED TRLHVMEFRG FEKFLQGRPI EEAPRIVPRI CGICDVQHHL AAAKAVDACF GFEPDDVLP AAYKMREIMN WGSYMHSHGL HFYFLAAPDF IAGKDRKTRN VFQIIKDAPD VALQAIELRK NALEIVRATG G RPIHPTSS TPGGISTELD DETQKDLLQK AQRNVELAEA TLELAVPIFE ENIDLVNSLG NIETYHTGLV KNGVWDVYDG IV RIKDKEG NLFREFKPAD YADTIAEHVK PYSWLKFPYI KDLGYPDGVY RVSPLSRLNV ADKMPDAAPK AQDYFKEFQD KFG YAQQTL LYHWARLIEV LACAECAADA LEGDLSGEKF PDSLERQAGD GVGIVEAPRG TLTHHYTCDE NGLITKANIV VATI QNNPA MEMGIQKVAQ DYIKPGVEVD DKIFNLMEMV IRAYDPCLSC ATHTIDSQMR LATLEVYDSE GDLVKRI

UniProtKB: F420-non-reducing hydrogenase subunit A

+
Macromolecule #13: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 45 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #14: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 14 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #15: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 15 / Number of copies: 2 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-9S8:
Non-cubane [4Fe-4S]-cluster

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Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 16 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,1...

MacromoleculeName: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
type: ligand / ID: 18 / Number of copies: 4 / Formula: MGD
Molecular weightTheoretical: 740.557 Da
Chemical component information

ChemComp-MGD:
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE

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Macromolecule #19: MOLYBDENUM ATOM

MacromoleculeName: MOLYBDENUM ATOM / type: ligand / ID: 19 / Number of copies: 2 / Formula: MO
Molecular weightTheoretical: 95.94 Da
Chemical component information

ChemComp-MO:
MOLYBDENUM ATOM

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Macromolecule #20: HYDROSULFURIC ACID

MacromoleculeName: HYDROSULFURIC ACID / type: ligand / ID: 20 / Number of copies: 2 / Formula: H2S
Molecular weightTheoretical: 34.081 Da
Chemical component information

ChemComp-H2S:
HYDROSULFURIC ACID

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Macromolecule #21: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 21 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #22: CARBONMONOXIDE-(DICYANO) IRON

MacromoleculeName: CARBONMONOXIDE-(DICYANO) IRON / type: ligand / ID: 22 / Number of copies: 1 / Formula: FCO
Molecular weightTheoretical: 135.89 Da
Chemical component information

ChemComp-FCO:
CARBONMONOXIDE-(DICYANO) IRON

+
Macromolecule #23: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

+
Macromolecule #24: water

MacromoleculeName: water / type: ligand / ID: 24 / Number of copies: 343 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThe buffer is pH 7.6 100 mM sodium phosphate with 150 mM NaCl, and containing 2 mM DTT

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 18777 / Average exposure time: 3.55 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 917008
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Particles had been C2-symmetry expanded. It is a composite map
Number images used: 722594
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2
Details: 3D-classification without alignment with RELION used before final local refinements and CTF correction

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Generated using ModelAngelo
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9sw6:
Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marburgensis (composite structure)

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