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- EMDB-12206: Formate dehydrogenase - heterodisulfide reductase - formylmethano... -

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Basic information

Entry
Database: EMDB / ID: EMD-12206
TitleFormate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (hexameric, composite structure)
Map data
Sample
  • Complex: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
    • Protein or peptide: x 12 types
  • Ligand: x 7 types
Keywordsmethanogenesis / flavin-based electron bifurcation / CO2-fixation / formate dehydrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate metabolic process / methanogenesis, from carbon dioxide / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis ...formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate metabolic process / methanogenesis, from carbon dioxide / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / formate dehydrogenase (NAD+) activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdopterin cofactor binding / NADH dehydrogenase activity / iron-sulfur cluster binding / transition metal ion binding / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / membrane / plasma membrane
Similarity search - Function
Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit B / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / : / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / FAD dependent oxidoreductase ...Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit B / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / : / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / FAD dependent oxidoreductase / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / Amidohydrolase 3 / Amidohydrolase family / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 2. / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / : / Molybdopterin oxidoreductase, prokaryotic, conserved site / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Metal-dependent hydrolase, composite domain superfamily / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 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
F420-non-reducing hydrogenase subunit D / CoB--CoM heterodisulfide reductase iron-sulfur subunit A / CoB--CoM heterodisulfide reductase subunit B / CoB--CoM heterodisulfide reductase subunit C / Formylmethanofuran dehydrogenase, subunit F / Formylmethanofuran dehydrogenase, subunit G / Formate dehydrogenase, beta subunit (F420) / Formylmethanofuran dehydrogenase, subunit D / Formate dehydrogenase, alpha subunit (F420) / formylmethanofuran dehydrogenase ...F420-non-reducing hydrogenase subunit D / CoB--CoM heterodisulfide reductase iron-sulfur subunit A / CoB--CoM heterodisulfide reductase subunit B / CoB--CoM heterodisulfide reductase subunit C / Formylmethanofuran dehydrogenase, subunit F / Formylmethanofuran dehydrogenase, subunit G / Formate dehydrogenase, beta subunit (F420) / Formylmethanofuran dehydrogenase, subunit D / Formate dehydrogenase, alpha subunit (F420) / formylmethanofuran dehydrogenase / Formylmethanofuran dehydrogenase, subunit A / formylmethanofuran dehydrogenase subunit B
Similarity search - Component
Biological speciesMethanospirillum hungatei JF-1 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPfeil-Gardiner O / Watanabe T
Funding support Germany, Japan, 4 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SH 87/1-1 Germany
Japan Society for the Promotion of Science (JSPS) Japan
Alexander von Humboldt Foundation Germany
CitationJournal: Science / Year: 2021
Title: Three-megadalton complex of methanogenic electron-bifurcating and CO-fixing enzymes.
Authors: Tomohiro Watanabe / Olivia Pfeil-Gardiner / Jörg Kahnt / Jürgen Koch / Seigo Shima / Bonnie J Murphy /
Abstract: The first reaction of the methanogenic pathway from carbon dioxide (CO) is the reduction and condensation of CO to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly ...The first reaction of the methanogenic pathway from carbon dioxide (CO) is the reduction and condensation of CO to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly reducing electrons for this reaction are generated by heterodisulfide reductase (Hdr) in complex with hydrogenase or formate dehydrogenase (Fdh) using a flavin-based electron-bifurcation mechanism. Here, we report enzymological and structural characterizations of Fdh-Hdr-Fmd complexes from . The complexes catalyze this reaction using electrons from formate and the reduced form of the electron carrier F. Conformational changes in HdrA mediate electron bifurcation, and polyferredoxin FmdF directly transfers electrons to the CO reduction site, as evidenced by methanofuran-dependent flavin-based electron bifurcation even without free ferredoxin, a diffusible electron carrier between Hdr and Fmd. Conservation of Hdr and Fmd structures suggests that this complex is common among hydrogenotrophic methanogens.
History
DepositionJan 15, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bkb
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bkb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12206.png

Downloads & links

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Map

FileDownload / File: emd_12206.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.68 Å/pix.
x 320 pix.
= 537.6 Å		1.68 Å/pix.
x 320 pix.
= 537.6 Å		1.68 Å/pix.
x 320 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-31.762011999999999 - 84.060310000000001
Average (Standard dev.)0.04726489 (±1.829393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-31.76284.0600.047

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Supplemental data

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Sample components

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Entire : Dimeric formate dehydrogenase - heterodisulfide reductase - formy...

EntireName: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
Components
  • Complex: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
    • Protein or peptide: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
    • Protein or peptide: F420-non-reducing hydrogenase subunit D
    • Protein or peptide: Formate dehydrogenase, beta subunit (F420)
    • Protein or peptide: CoB--CoM heterodisulfide reductase subunit C
    • Protein or peptide: CoB--CoM heterodisulfide reductase subunit B
    • Protein or peptide: Formate dehydrogenase
    • Protein or peptide: Formylmethanofuran dehydrogenase
    • Protein or peptide: Formylmethanofuran dehydrogenase, subunit G
    • Protein or peptide: Formylmethanofuran dehydrogenase, subunit A
    • Protein or peptide: Formylmethanofuran dehydrogenase, subunit D
    • Protein or peptide: Formylmethanofuran dehydrogenase, subunit F
    • Protein or peptide: Formylmethanofuran dehydrogenase, subunit B
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: ZINC ION
  • Ligand: MOLYBDENUM ATOM
  • 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

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Supramolecule #1: Dimeric formate dehydrogenase - heterodisulfide reductase - formy...

SupramoleculeName: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea) / Location in cell: cytoplasm
Molecular weightTheoretical: 948 KDa

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Macromolecule #1: CoB--CoM heterodisulfide reductase iron-sulfur subunit A

MacromoleculeName: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on a sulfur group of donors
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 72.885062 KDa
SequenceString: MAENTEPRIG VFVCHCGTNI AGSMSIDDVV NYAKTLPYVA VADQYQYMCS TPGQKKIDDA IKEYNLTGVV VAACSPRLHE PTFRTATKE GGLNPFRFEM ANIREQNSWV HMHGMWDEAT QKAKDQVRMA VAKAAKLEDL VPKSVPVEKT AMVVGGGVAG M QAALDLAS ...String:
MAENTEPRIG VFVCHCGTNI AGSMSIDDVV NYAKTLPYVA VADQYQYMCS TPGQKKIDDA IKEYNLTGVV VAACSPRLHE PTFRTATKE GGLNPFRFEM ANIREQNSWV HMHGMWDEAT QKAKDQVRMA VAKAAKLEDL VPKSVPVEKT AMVVGGGVAG M QAALDLAS AGIKTYLIER TPTIGGRMSQ LDKTFPTLDC SQCILTPKMV DVGRHPNIEM MTYTEVEKVE GYIGNFDVTL RK KARGVLT PTEATAKGIV GGGCNGCGDC SAVCPVIKPN PFEMGMAPRK AIYIYHAQVM PLIYTVDFDS CVKCGLCVEA CGD KKAIDL EMQDEFITVK VGTAVLATGY ELFPIENKRE WGYKQFDNVI NALEFERLIC ASGPTGGHLV RPSDGKTPMK VGFV LCAGS RDNTGIGKPY CSRFCCMYSL KHAHQIMEKI PGAVAYLFYM DIRSFGKMYE EFYYRIQHEG AKFIRGRVAN VLEDK ETKN LHVFTEDTLL GRPVDVEVDL LVLAAAVQPN EGANELRKKF GVSASQDGWM LEAHPKLNPC GTTTAGVFLA GVCQGP KDI PDTVAQAEGA ASAASIPIHM GEVELEPYFA MCIDELCAGC GMCVNLCPYS ALSLGEKNGR TVMVVTEAKC KGCGTCG GF CPGGAIKMQH FTTPQIVAQI DAFFAGGEQ

UniProtKB: CoB--CoM heterodisulfide reductase iron-sulfur subunit A

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Macromolecule #2: F420-non-reducing hydrogenase subunit D

MacromoleculeName: F420-non-reducing hydrogenase subunit D / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 15.692425 KDa
SequenceString:
MADDWKPQIL AIICNWCSYA GADLAGGARI QYPPTVRAIR VMCTGRVDML FILKAFVEGA DGVLVSGCHF GDCHYLEGNY KAAKRMFMI KNLLRNIGLD DRRFRMTFVS ASEGAKWGMV MEDVTNTIKE LGPSPIKEFK K

UniProtKB: F420-non-reducing hydrogenase subunit D

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Macromolecule #3: Formate dehydrogenase, beta subunit (F420)

MacromoleculeName: Formate dehydrogenase, beta subunit (F420) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 45.639895 KDa
SequenceString: MAAKGDMLYA WAKDAEIQKK GECGGAVTAL LKHALETKMV DAVVAIKKGK DLYDAVPTVI TNPEDIIQTA GSLHCGTLLI PKLIKKYLN GAKDMKLAVT CKGCDAMAFY ELAKRNQINL DNIIMIGVNC GGSVSPVTAR KMISNKFGVD PDTVHKEEID K GQFIIEYE ...String:
MAAKGDMLYA WAKDAEIQKK GECGGAVTAL LKHALETKMV DAVVAIKKGK DLYDAVPTVI TNPEDIIQTA GSLHCGTLLI PKLIKKYLN GAKDMKLAVT CKGCDAMAFY ELAKRNQINL DNIIMIGVNC GGSVSPVTAR KMISNKFGVD PDTVHKEEID K GQFIIEYE GGHKGIKIDE LEEEGYGRRS NCRRCKMKIP RQADIAAGNW GVIGDKAGKA TFLEICSEKG ANLVNSAQSK GA LEISPAD PKGIDIRAKV EKAMFNLGDE WRHRDFEGMG KGKDRLKLMM SESSKCIKCY ACVEACPICY CIECSTKKPW YIA PGVLPT SFMFHLIRFA HVSDSCINCG QCEELCPMEI PNALFMHSQQ VEIEKMFGHI PGQDMTPPIH AFVEEKAERA RLDA TGTDS IYTNIFTDE

UniProtKB: Formate dehydrogenase, beta subunit (F420)

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Macromolecule #4: CoB--CoM heterodisulfide reductase subunit C

MacromoleculeName: CoB--CoM heterodisulfide reductase subunit C / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 21.706963 KDa
SequenceString:
MAAKSYNIPE LDKKLADRRY HLSDTNPEFT QKILKTSRTI ANMCYQCGTC TGSCPSAPRS SYRIRLFMRR CVLGLENEAL TDPDLWLCT TCYSCTDRCP RDIAPTDVIM AMRNLAFKRD IVPKNFLQTV QLIYNSGHGV PNNDVNRAAR TKLGLPADPP T THSYPEFV KGIQKIIDHY ELKENADRIL KGD

UniProtKB: CoB--CoM heterodisulfide reductase subunit C

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Macromolecule #5: CoB--CoM heterodisulfide reductase subunit B

MacromoleculeName: CoB--CoM heterodisulfide reductase subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 32.930938 KDa
SequenceString: MHEYAFFLGC IAPNRYPGCE ASAIKTSEKV GIKLLPLKGA SCCPAPGAFG SIDLNVWYAM AARNLVLAEE MKKDIALICN GCYKSIWEV NHILKHNDEL RDNVNEVLAE IDMQFKGTID VWHLAELYYD DKVCGVQKIK DSVTTPLSGA KVAAHYGCHL M KPKKERHF ...String:
MHEYAFFLGC IAPNRYPGCE ASAIKTSEKV GIKLLPLKGA SCCPAPGAFG SIDLNVWYAM AARNLVLAEE MKKDIALICN GCYKSIWEV NHILKHNDEL RDNVNEVLAE IDMQFKGTID VWHLAELYYD DKVCGVQKIK DSVTTPLSGA KVAAHYGCHL M KPKKERHF GDTENPMWFE ELIGALGAEP IQYRNKMQCC GAGGGVRGYD IVHALDITNE KLINIQEAGA DAITELCPFC QL QFDRGQI EIKEKFGDVY NIPVLHYNEL LGLAQGMSPQ DLALDLHAID CTPFLQKVL

UniProtKB: CoB--CoM heterodisulfide reductase subunit B

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Macromolecule #6: Formate dehydrogenase

MacromoleculeName: Formate dehydrogenase / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 75.911445 KDa
SequenceString: MSENSEIMKY VATTCPYCGV GCTLNLVVSN GKVVGVEPNQ RSPINEGKLC PKGVTCWEHI HSPDRLTTPL IKKDGKFIEA SWDEALDLV AKNLKVIYDK HGPKGLGFQT SCRTVNEDCY IFQKFARVGF KTNNVDNCAR ICHGPSVAGL SLSFGSGAAT N GFEDALNA ...String:
MSENSEIMKY VATTCPYCGV GCTLNLVVSN GKVVGVEPNQ RSPINEGKLC PKGVTCWEHI HSPDRLTTPL IKKDGKFIEA SWDEALDLV AKNLKVIYDK HGPKGLGFQT SCRTVNEDCY IFQKFARVGF KTNNVDNCAR ICHGPSVAGL SLSFGSGAAT N GFEDALNA DLILIWGSNA VEAHPLAGRR IAQAKKKGIQ IIAVDPRYTM TARLADTYVR FNPSTHIALA NSMMYWIIKE GL EDKKFIQ DRVNGFEDLK KTVENYADAE AIHGVPLDVV KDIAFRYAKA KNAVIIYCLG ITELTTGTDN VRSMGNLALL TGN VGREGV GVNPLRGQNN VQGACDMGAY PNVYSGYQKC EVAENRAKME KAWSVTNLPD WYGATLTEQI NQCGDEIKGM YILG LNPVV TYPSSNHVKA QLEKLDFLVV QDIFFTETCQ YADVILPGAC FAEKDGTFTS GERRINRVRK AVNPPGQAKE DIHII SELA AKMGFKGFEL PTAKDVWDDM RAVTPSMFGA TYEKLERPEG ICWPCPTEEH PGTPILHREK FATADGKGNL FGIDYR PPA EVADAEYPFT LMTGRLIFHY HSRTQTDRAA DLHREVPESY AQINIEDARR LGIKNNEYIK LKSRRGETTT LARVTDE VA PGVVYMTMHF ADGVNNLTNT VLDPMSKMPE LKHCAISIEK VGGN

UniProtKB: Formate dehydrogenase, alpha subunit (F420)

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Macromolecule #7: Formylmethanofuran dehydrogenase

MacromoleculeName: Formylmethanofuran dehydrogenase / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 28.696902 KDa
SequenceString: METITMTLVQ EPELFLECYS VTPDLFAGKS LAEIADLPAH EGKIQWKLGD FFKFEGKAGE TAADTKIVVN GNVRRMKRFG QQMTAGEII INSDADMYIG GWMKGGKITV KGNADSFLGI AMEGGEILIE GDAQNHVGSA YRGDWRGMSG GLIRVKGKAG N DIGTAMTG ...String:
METITMTLVQ EPELFLECYS VTPDLFAGKS LAEIADLPAH EGKIQWKLGD FFKFEGKAGE TAADTKIVVN GNVRRMKRFG QQMTAGEII INSDADMYIG GWMKGGKITV KGNADSFLGI AMEGGEILIE GDAQNHVGSA YRGDWRGMSG GLIRVKGKAG N DIGTAMTG GTIIIEGDAF IHVLTHAEGG TVIIKGDVEG RVGGQMVKGD AYILGNLLYP LPGFKKVATV EKEVDGATYT FD QFIGDLG ERKEKKKGEI IYGNIFLKK

UniProtKB: formylmethanofuran dehydrogenase

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Macromolecule #8: Formylmethanofuran dehydrogenase, subunit G

MacromoleculeName: Formylmethanofuran dehydrogenase, subunit G / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 16.38802 KDa
SequenceString:
MKYRGPEDKL IVFTFYKESK KKRHFFPFFL QKISYLFQNI YLYFLTTFVQ SILIDQAGAT NMAFAVHVNM ERCTGCNNCV VACPVNALE LNTVNPSSTD KIYKVINGDA VILDVKHELC AGCGICVDAC PYDVIQLSGQ PPQAVEA

UniProtKB: Formylmethanofuran dehydrogenase, subunit G

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Macromolecule #9: Formylmethanofuran dehydrogenase, subunit A

MacromoleculeName: Formylmethanofuran dehydrogenase, subunit A / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 63.636211 KDa
SequenceString: MSELLIKNGY IFDPISGIKG DKADIAIKDG KIVDKVSSKA QVIDASGKTV MSGGVDIHTH VSGPKVNTGR MMRPEDKFFR GSYRGGIIK QGKRMEMGFS IPSTYKTGYA YARMGYTFTN EAAMPPLLAP HVHEEFRDTP ILDQAAMPVF GNNWFCFEYI K NKELENNA ...String:
MSELLIKNGY IFDPISGIKG DKADIAIKDG KIVDKVSSKA QVIDASGKTV MSGGVDIHTH VSGPKVNTGR MMRPEDKFFR GSYRGGIIK QGKRMEMGFS IPSTYKTGYA YARMGYTFTN EAAMPPLLAP HVHEEFRDTP ILDQAAMPVF GNNWFCFEYI K NKELENNA AYVAWLLNAT KGIGI(KCX)VVNP GGTEAWAWGE NCTTINDPVP YFDITPAEIV KGLIETNEYL GLPHSVHI H GNNLGNPGNY KDTLDTLRLA ESYKAKNKFG REQVLHNTHI QFHSYKGTSW ADFESGAKEI MDYVNANKNI TCDIGQVTL DETTTMTADG PFEYHLNQLN HIKWANVDVE LETGSGVVPY IYDKNIKVCG IQWAIGLELA LYAKDLMRVH ITTDHPNAGP FTRYPCVIK WLMSEKARKA TLDTMKWKDK VIAASNIASM DRELGLYEIA MMTRAGPAKA LGLAAIYGSL VKGADGNVAI Y NLDANDLP SDPELIEAAF QNTAYTIKEG VVVVKDGEII AEPHKYTLWT KVNMPENAQV MHDIKEKFTK NYTVNLENYA VF DEHVHNP RAIELDVA

UniProtKB: Formylmethanofuran dehydrogenase, subunit A

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Macromolecule #10: Formylmethanofuran dehydrogenase, subunit D

MacromoleculeName: Formylmethanofuran dehydrogenase, subunit D / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 15.157499 KDa
SequenceString:
MKAKKTLNMI TQRAVEEGIA MEIGKTSRQY FDACSIIEMN EQDMKELGIM KNTNVRVKSE SGEVVVKAVV GRQTCYPGLC HIRQGVWAN QVVPPRTQST GAPQYSGFPV TVEPVPNERL KTALELVQGA VGMWKGDQ

UniProtKB: Formylmethanofuran dehydrogenase, subunit D

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Macromolecule #11: Formylmethanofuran dehydrogenase, subunit F

MacromoleculeName: Formylmethanofuran dehydrogenase, subunit F / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 42.216734 KDa
SequenceString: MSTLFPKYSK TTDGSKVIME QRLLQQVNNL ILDNDICTGC GICSEVCPEE AISVGAVGGV RRGLVDDAAS IHVDETKCSY CGVCVIMCP FSALALKVDG EERLPILEKE GFPTYDKGTA IDQDKCVRCN ICDDVCPRDA IDRDVPLFEG EDKEGLAKGQ A VELKIEFK ...String:
MSTLFPKYSK TTDGSKVIME QRLLQQVNNL ILDNDICTGC GICSEVCPEE AISVGAVGGV RRGLVDDAAS IHVDETKCSY CGVCVIMCP FSALALKVDG EERLPILEKE GFPTYDKGTA IDQDKCVRCN ICDDVCPRDA IDRDVPLFEG EDKEGLAKGQ A VELKIEFK VDDEKCTKCG ICGNLCEAIN VLHKPFSPEI GKVEGEVIWD EAYCDGCNVC AEACPSEAIK VTRTVVGQKK LG NVNIIDE DCCTCRWCAI NCPTEAITVN KIFEGEITFH AEKCPGGCST CVDVCPANAI YLPTPKPAKD MKGQIEAKIA VNK DFCILC GACVNACPGE DIIYLRRDSV KIKGKETDLF KKIKEKLFTP RTSKVKEQPS LAGSVELKAV SQ

UniProtKB: Formylmethanofuran dehydrogenase, subunit F

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Macromolecule #12: Formylmethanofuran dehydrogenase, subunit B

MacromoleculeName: Formylmethanofuran dehydrogenase, subunit B / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 49.371586 KDa
SequenceString: MPKVIENVGC PYCGCSCDDV RITVSDDGKD ILEVENVCAI GTEIFKHGCS KDRIRLPRMR QPDGSMKDIS YEEAIDWTAR HLLKAKKPL MYGFGSTNCE GQAAAARVME IAGGMLDNCA TICHGPSFLA IFDNGYPSCT LGEVKNRADV IVYWGSNPAH A HPRHMSRY ...String:
MPKVIENVGC PYCGCSCDDV RITVSDDGKD ILEVENVCAI GTEIFKHGCS KDRIRLPRMR QPDGSMKDIS YEEAIDWTAR HLLKAKKPL MYGFGSTNCE GQAAAARVME IAGGMLDNCA TICHGPSFLA IFDNGYPSCT LGEVKNRADV IVYWGSNPAH A HPRHMSRY SIFPRGFFTG KGQKKRTVIV IDPRFTDTAN VADYHLQVKQ GHDYELFNAF RMVIHGHGKD LPDEVAGIKK ET ILEVAEI MKNARFGTTF FGMGLTHTDG RNHNIDIAIS LTRDLNKISK WTIMAMRGHY NIAGPGVVWS WTFGFPYCLD LTK QNHAHM NPGETSSVDM AMRDEVDMFI NIGTDAAAHF PIPAVKQLKK HPWVTIDPSI NMASEISDLH IPVCICGVDV GGIV YRMDN VPIQFRKVIE PPEGVMDDET LLNKIADRME ELKAKGEA

UniProtKB: formylmethanofuran dehydrogenase subunit B

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Macromolecule #13: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 48 / 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: 4 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

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

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Macromolecule #15: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 15 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #16: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 16 / Number of copies: 4 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

MacromoleculeName: MOLYBDENUM ATOM / type: ligand / ID: 18 / Number of copies: 2 / Formula: MO
Molecular weightTheoretical: 95.94 Da
Chemical component information

ChemComp-MO:
MOLYBDENUM ATOM

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Macromolecule #19: 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: 19 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.6 / Component - Concentration: 25.0 mM / Component - Formula: Tris-HCl / Component - Name: Tris-HCl
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 293 K / Instrument: HOMEMADE PLUNGER
DetailsPreparation in an anaerobic tent (O2 < 20 ppm at all times, nearly always < 2ppm)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8745 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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

DetailsRecorded in counted mode
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1.13), RELION (ver. 3.1)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: This is a composite map. The maps that constitute this composite map have resolutions between 3.4 and 4.0 A. These have all been determined by FSC 0.143 cut-off.
Number images used: 203264

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7bkb:
Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (hexameric, composite structure)

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