[English] 日本語
Yorodumi
- PDB-7qv7: Cryo-EM structure of Hydrogen-dependent CO2 reductase. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qv7
TitleCryo-EM structure of Hydrogen-dependent CO2 reductase.
Components(Hydrogen dependent carbon dioxide reductase subunit ...) x 4
KeywordsELECTRON TRANSPORT / Hydrogen-dependent CO2 reduction / Carbon fixation / Protein nanowire filament / enzyme catalysis
Function / homology
Function and homology information


formate metabolic process / formate dehydrogenase / ferredoxin hydrogenase / formate dehydrogenase (NAD+) activity / Oxidoreductases / ferredoxin hydrogenase activity / molybdopterin cofactor binding / NADH dehydrogenase activity / iron-sulfur cluster binding / respiratory electron transport chain ...formate metabolic process / formate dehydrogenase / ferredoxin hydrogenase / formate dehydrogenase (NAD+) activity / Oxidoreductases / ferredoxin hydrogenase activity / molybdopterin cofactor binding / NADH dehydrogenase activity / iron-sulfur cluster binding / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / membrane
Similarity search - Function
Formate dehydrogenase H, molybdopterin-binding domain / 4Fe-4S binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain ...Formate dehydrogenase H, molybdopterin-binding domain / 4Fe-4S binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 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 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-402 / IRON/SULFUR CLUSTER / Hydrogen dependent carbon dioxide reductase subunit HydA2 / Hydrogen dependent carbon dioxide reductase subunit HycB3 / Hydrogen dependent carbon dioxide reductase subunit FdhF / Hydrogen dependent carbon dioxide reductase subunit HycB4
Similarity search - Component
Biological speciesThermoanaerobacter kivui (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDietrich, H.M. / Righetto, R.D. / Kumar, A. / Wietrzynski, W. / Schuller, S.K. / Trischler, R. / Wagner, J. / Schwarz, F.M. / Engel, B.D. / Mueller, V. / Schuller, J.M.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3364/1-1 Germany
European Research Council (ERC)741791European Union
German Research Foundation (DFG)FOR 2092 Germany
Alexander von Humboldt Foundation Germany
German Research Foundation (DFG)20016/446 Germany
CitationJournal: Nature / Year: 2022
Title: Membrane-anchored HDCR nanowires drive hydrogen-powered CO fixation.
Authors: Helge M Dietrich / Ricardo D Righetto / Anuj Kumar / Wojciech Wietrzynski / Raphael Trischler / Sandra K Schuller / Jonathan Wagner / Fabian M Schwarz / Benjamin D Engel / Volker Müller / Jan M Schuller /
Abstract: Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO ...Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO fixation-hydrogen-dependent CO reductase (HDCR)-which directly converts H and CO into formic acid. HDCR reduces CO with a higher activity than any other known biological or chemical catalyst, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.
History
DepositionJan 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.0Jul 6, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 6, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 6, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 6, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 6, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 6, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 6, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 10, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 1, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydrogen dependent carbon dioxide reductase subunit HycB3
B: Hydrogen dependent carbon dioxide reductase subunit HycB4
C: Hydrogen dependent carbon dioxide reductase subunit HycB4
D: Hydrogen dependent carbon dioxide reductase subunit HydA2
G: Hydrogen dependent carbon dioxide reductase subunit HycB3
J: Hydrogen dependent carbon dioxide reductase subunit HycB4
K: Hydrogen dependent carbon dioxide reductase subunit HydA2
N: Hydrogen dependent carbon dioxide reductase subunit HycB4
P: Hydrogen dependent carbon dioxide reductase subunit HycB4
Q: Hydrogen dependent carbon dioxide reductase subunit HydA2
R: Hydrogen dependent carbon dioxide reductase subunit HydA2
S: Hydrogen dependent carbon dioxide reductase subunit FdhF
V: Hydrogen dependent carbon dioxide reductase subunit HydA2
X: Hydrogen dependent carbon dioxide reductase subunit HycB4
Y: Hydrogen dependent carbon dioxide reductase subunit FdhF
Z: Hydrogen dependent carbon dioxide reductase subunit HydA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)673,36374
Polymers652,94816
Non-polymers20,41558
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Hydrogen dependent carbon dioxide reductase subunit ... , 4 types, 16 molecules AGBCJNPXDKQRVZSY

#1: Protein Hydrogen dependent carbon dioxide reductase subunit HycB3


Mass: 20520.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) / References: UniProt: A0A097ATJ9, Oxidoreductases
#2: Protein
Hydrogen dependent carbon dioxide reductase subunit HycB4


Mass: 23052.180 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) / References: UniProt: A0A097ATK6, Oxidoreductases
#3: Protein
Hydrogen dependent carbon dioxide reductase subunit HydA2


Mass: 51430.270 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) / References: UniProt: A0A097ATH7, ferredoxin hydrogenase
#4: Protein Hydrogen dependent carbon dioxide reductase subunit FdhF


Mass: 82505.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) / References: UniProt: A0A097ATK5, formate dehydrogenase

-
Non-polymers , 2 types, 58 molecules

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


Mass: 351.640 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-402 / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)


Mass: 354.953 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Hydrogen-dependent CO2 reductase (HDCR) complex with iron-sulphur clusters and the H-cluster.
Type: COMPLEX
Details: A single functional unit of HDCR complex consists of 4 subunits - FdhF, HydA2, HycB3, and HycB4(1)
Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Thermoanaerobacter kivui LKT-1 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 719937 / Symmetry type: POINT

+
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