[English] 日本語
Yorodumi
- PDB-9t1s: Heterodisulfide-Hydrogenase-Formate Dehydrogenase dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9t1s
TitleHeterodisulfide-Hydrogenase-Formate Dehydrogenase dimer
Components
  • (F420-non-reducing hydrogenase ...) x 2
  • (formate dehydrogenase (coenzyme ...) x 2
  • CoB--CoM heterodisulfide reductase iron-sulfur subunit A
  • Coenzyme F420-reducing hydrogenase, alpha subunit
  • F420 non-reducing hydrogenase subunit
  • H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2
  • Heterodisulfide reductase subunit B
KeywordsELECTRON TRANSPORT / Methanogenesis / Super-assembly / Flavin-based electron bifurcation / heterodisulfide-reductase / polyferredoxin / formylmethanofuran dehydrogenase / oxidoreductase
Function / homology
Function and homology information


formate:CoB-CoM heterodisulfide,ferredoxin reductase / hydrogen dehydrogenase / formate dehydrogenase (coenzyme F420) / formate dehydrogenase (coenzyme F420) activity / hydrogen dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / formate metabolic process / CoB--CoM heterodisulfide reductase activity / formate dehydrogenase (NAD+) activity ...formate:CoB-CoM heterodisulfide,ferredoxin reductase / hydrogen dehydrogenase / formate dehydrogenase (coenzyme F420) / formate dehydrogenase (coenzyme F420) activity / hydrogen dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / formate metabolic process / CoB--CoM heterodisulfide reductase activity / formate dehydrogenase (NAD+) activity / methanogenesis / ferredoxin hydrogenase activity / molybdopterin cofactor binding / nickel cation binding / NADH dehydrogenase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / : / Formate dehydrogenase H, molybdopterin-binding domain / HoxL-like / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / CoB--CoM heterodisulphide reductase, subunit C / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / Prokaryotic molybdopterin oxidoreductases signature 2. ...: / : / Formate dehydrogenase H, molybdopterin-binding domain / HoxL-like / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / CoB--CoM heterodisulphide reductase, subunit C / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / Prokaryotic molybdopterin oxidoreductases signature 2. / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenase, large subunit, nickel binding site / Molybdopterin oxidoreductase Fe4S4 domain / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 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 / : / F420 non-reducing hydrogenase subunit ...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 / : / F420 non-reducing hydrogenase subunit / F420-non-reducing hydrogenase subunit delta / : / : / : / formate dehydrogenase (coenzyme F420) / H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2
Similarity search - Component
Biological speciesMethanococcus maripaludis (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
DepositionOct 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
B: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
C: Heterodisulfide reductase subunit B
D: Heterodisulfide reductase subunit B
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
H: F420-non-reducing hydrogenase small subunit
I: F420-non-reducing hydrogenase subunit delta
J: F420-non-reducing hydrogenase subunit delta
K: F420 non-reducing hydrogenase subunit
L: formate dehydrogenase (coenzyme F420)
M: formate dehydrogenase (coenzyme F420)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,27550
Polymers473,86113
Non-polymers14,41437
Water00
1


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

-
Components

-
Protein , 4 types, 7 molecules ABCDEFG

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


Mass: 71360.758 Da / Num. of mol.: 2 / 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
#2: Protein Heterodisulfide reductase subunit B


Mass: 32062.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A7J9NT94, dihydromethanophenazine:CoB-CoM heterodisulfide 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.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: Q6LYD7, H2:CoB-CoM heterodisulfide,ferredoxin reductase, formate:CoB-CoM heterodisulfide,ferredoxin reductase
#4: Protein Coenzyme F420-reducing hydrogenase, alpha subunit / F420-non-reducing hydrogenase large subunit


Mass: 45687.258 Da / Num. of mol.: 1 / 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

-
F420-non-reducing hydrogenase ... , 2 types, 3 molecules HIJ

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


Mass: 30787.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A7J9P3N2, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
#6: Protein F420-non-reducing hydrogenase subunit delta


Mass: 14675.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae / References: UniProt: A0A2L1CBC1

-
Protein/peptide , 1 types, 1 molecules K

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


Mass: 3119.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae / References: UniProt: A0A2L1CB29

-
Formate dehydrogenase (coenzyme ... , 2 types, 2 molecules LM

#8: Protein formate dehydrogenase (coenzyme F420)


Mass: 74353.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: M9QXF8, formate dehydrogenase (coenzyme F420)
#9: Protein formate dehydrogenase (coenzyme F420)


Mass: 42748.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanococcus maripaludis (archaea) / Strain: deltae
References: UniProt: A0A7J9PDY4, formate dehydrogenase (coenzyme F420)

-
Non-polymers , 7 types, 37 molecules

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


Mass: 351.640 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#12: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 194.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2NiO / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#16: 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.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly
Type: COMPLEX / Entity ID: #1-#7, #9, #8 / 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 ?Mflavin adenine dinucleotideC27H33N9O15P21
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)

-
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)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
9PHENIX1.19_4158model refinement
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_d0.00434294
ELECTRON MICROSCOPYf_angle_d0.68346637
ELECTRON MICROSCOPYf_dihedral_angle_d13.70512781
ELECTRON MICROSCOPYf_chiral_restr0.055220
ELECTRON MICROSCOPYf_plane_restr0.0076014

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more