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Basic information

Entry
Database: PDB / ID: 9sfi
TitleHeterodisulfide reductase-Formylmethanofuran dehydrogenase super-assembly
Components
  • (F420-non-reducing hydrogenase ...) x 2
  • (Formylmethanofuran dehydrogenase subunit ...) x 2
  • (H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit ...) x 2
  • 4Fe-4S binding protein
  • 4Fe-4S ferredoxin
  • CoB--CoM heterodisulfide reductase iron-sulfur subunit A
  • Coenzyme F420-reducing hydrogenase, alpha subunit
  • F420 non-reducing hydrogenase subunit
  • Ferredoxin
  • Molybdopterin oxidoreductase
  • Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
KeywordsELECTRON TRANSPORT / Methanogenesis / Super-assembly / Flavin-based elctron bifurcation / Heterodisulfide-reductase / Polyferredoxin / Formylmethanofuran dehydrogenase
Function / homology
Function and homology information


formate:CoB-CoM heterodisulfide,ferredoxin reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / methanogenesis / ferredoxin hydrogenase activity / nickel cation binding / 2 iron, 2 sulfur cluster binding ...formate:CoB-CoM heterodisulfide,ferredoxin reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / methanogenesis / ferredoxin hydrogenase activity / nickel cation binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / plasma membrane
Similarity search - Function
: / : / : / HoxL-like / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / Methyl-viologen-reducing hydrogenase, delta subunit ...: / : / : / HoxL-like / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Alpha-helical ferredoxin / 4Fe-4S binding domain / [NiFe]-hydrogenase, large subunit / 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
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / Chem-NFU / IRON/SULFUR CLUSTER / : / Coenzyme F420-reducing hydrogenase, alpha subunit / : / Ferredoxin ...Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / Chem-NFU / IRON/SULFUR CLUSTER / : / Coenzyme F420-reducing hydrogenase, alpha subunit / : / Ferredoxin / : / F420 non-reducing hydrogenase subunit / F420-non-reducing hydrogenase subunit delta / : / : / : / : / : / : / H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2 / H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
Methanococcus maripaludis deltae (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsPaul, S. / Schuller, J.M.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)505997786 Germany
European Research Council (ERC)101075992European Union
CitationJournal: To Be Published
Title: An eight-megadalton super assembly links the first and the last step in methanogenesis to power CO2 reduction
Authors: Paul, S. / Schuller, J.M.
History
DepositionAug 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
B: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
C: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2
D: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2
E: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2
F: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2
I: F420-non-reducing hydrogenase small subunit
J: F420-non-reducing hydrogenase small subunit
K: F420-non-reducing hydrogenase subunit delta
L: F420-non-reducing hydrogenase subunit delta
M: F420 non-reducing hydrogenase subunit
N: F420 non-reducing hydrogenase subunit
O: Ferredoxin
P: Formylmethanofuran dehydrogenase subunit A
Q: Molybdopterin oxidoreductase
R: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
S: Formylmethanofuran dehydrogenase subunit D
T: 4Fe-4S ferredoxin
U: 4Fe-4S binding protein
a: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
b: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
c: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2
d: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2
e: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2
f: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2
g: Coenzyme F420-reducing hydrogenase, alpha subunit
i: F420-non-reducing hydrogenase small subunit
j: F420-non-reducing hydrogenase small subunit
k: F420-non-reducing hydrogenase subunit delta
l: F420-non-reducing hydrogenase subunit delta
m: F420 non-reducing hydrogenase subunit
n: F420 non-reducing hydrogenase subunit
o: Ferredoxin
p: Formylmethanofuran dehydrogenase subunit A
q: Molybdopterin oxidoreductase
r: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
s: Formylmethanofuran dehydrogenase subunit D
t: 4Fe-4S ferredoxin
u: 4Fe-4S binding protein
G: Coenzyme F420-reducing hydrogenase, alpha subunit
H: Coenzyme F420-reducing hydrogenase, alpha subunit
h: Coenzyme F420-reducing hydrogenase, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,404,230164
Polymers1,360,85042
Non-polymers43,379122
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 18 molecules ABabOoQqRrTtUugGHh

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


Mass: 71360.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A2L1CB19, Oxidoreductases; Acting on a sulfur group of donors
#7: Protein Ferredoxin


Mass: 42128.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae / References: UniProt: A0A2L1CB03
#9: Protein Molybdopterin oxidoreductase


Mass: 48582.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae / References: UniProt: A0A2L1CAZ7
#10: Protein Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C / Tungsten-containing formylmethanofuran dehydrogenase II subunit C


Mass: 29204.713 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A2L1CC77, formylmethanofuran dehydrogenase
#12: Protein 4Fe-4S ferredoxin / NADH-quinone oxidoreductase subunit I


Mass: 38257.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A2L1CC83, NADH dehydrogenase (quinone)
#13: Protein 4Fe-4S binding protein / 4Fe-4S ferredoxin / NADH dehydrogenase subunit I


Mass: 8351.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae / References: UniProt: A0A2L1CCM5
#14: Protein
Coenzyme F420-reducing hydrogenase, alpha subunit / F420-non-reducing hydrogenase large subunit


Mass: 45687.258 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A2L1CAX5, hydrogen dehydrogenase, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors

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H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit ... , 2 types, 8 molecules CDcdEFef

#2: Protein
H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2 / CoB--CoM heterodisulfide reductase subunit B2


Mass: 32062.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: Q6LYD8, H2:CoB-CoM heterodisulfide,ferredoxin reductase, formate:CoB-CoM heterodisulfide,ferredoxin reductase
#3: Protein
H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2 / CoB--CoM heterodisulfide reductase iron-sulfur subunit C2


Mass: 20483.850 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea)
References: UniProt: Q6LYD7, H2:CoB-CoM heterodisulfide,ferredoxin reductase, formate:CoB-CoM heterodisulfide,ferredoxin reductase

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F420-non-reducing hydrogenase ... , 2 types, 8 molecules IJijKLkl

#4: Protein
F420-non-reducing hydrogenase small subunit


Mass: 30787.498 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Methanococcus maripaludis deltae (archaea)
References: UniProt: A0A7J9P3N2, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
#5: Protein
F420-non-reducing hydrogenase subunit delta


Mass: 14675.697 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae / References: UniProt: A0A2L1CBC1

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Protein/peptide , 1 types, 4 molecules MNmn

#6: Protein/peptide
F420 non-reducing hydrogenase subunit


Mass: 3119.515 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae / References: UniProt: A0A2L1CB29

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Formylmethanofuran dehydrogenase subunit ... , 2 types, 4 molecules PpSs

#8: Protein Formylmethanofuran dehydrogenase subunit A


Mass: 63386.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A7J9NZ09, formylmethanofuran dehydrogenase
#11: Protein Formylmethanofuran dehydrogenase subunit D / Nitrate reductase


Mass: 14159.315 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A2L1CCC1, formylmethanofuran dehydrogenase, nitrate reductase

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Non-polymers , 8 types, 122 molecules

#15: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 92 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#17: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical
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 / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 194.583 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3FeN2NiO / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Eight-megadalton assembly of Heterodisulfide reductase- Vhu Hydrogenase- Formylmethanofuran dehydrogenase
Type: COMPLEX / Entity ID: #1-#3, #14, #4-#13 / Source: NATURAL
Molecular weightValue: 8 MDa / Experimental value: YES
Source (natural)Organism: Methanococcus maripaludis S2 (archaea)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaCl1
312.5 mMmagnesium chlorideMgCl21
420 uMFlavine-adenine-dinucleotideC27H33N9O15P1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 279 K
Details: Vitrification under strict anaerobic conditions inside a Coy Lab's Vinyl anaerobic chamber (95% N2/ 5% H2)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110231 / Symmetry type: POINT
RefinementHighest resolution: 4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00398780
ELECTRON MICROSCOPYf_angle_d0.915134960
ELECTRON MICROSCOPYf_dihedral_angle_d13.68736558
ELECTRON MICROSCOPYf_chiral_restr0.04315142
ELECTRON MICROSCOPYf_plane_restr0.00517130

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