[English] 日本語
Yorodumi
- PDB-9h1l: Methyl-coenzyme M reductase activation complex binding to the A2 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h1l
TitleMethyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP
Components
  • (Methanogenesis marker protein ...) x 2
  • (Methyl-coenzyme M reductase subunit ...) x 3
  • DUF2098 domain-containing protein
  • Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA
  • Methyl-coenzyme M reductase operon protein C
  • UPF0288 protein MmarC6_0796
KeywordsOXIDOREDUCTASE / Methyl-coenzyme M reductase / activation complex / ATPase / Iron-sulfur clusters
Function / homology
Function and homology information


organic phosphonate catabolic process / coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Methyl coenzyme M reductase system, component A2 / Methyl-coenzyme M reductase, protein C / Uncharacterised conserved protein UCP019164, methanogenesis / Uncharacterised protein family UPF0288, methanogenesis / Uncharacterised conserved protein UCP019464, methanogenesis / Uncharacterised conserved protein UCP037053 / Protein of unknown function DUF2098 / Methyl-coenzyme M reductase, protein C-like / Methyl-coenzyme M reductase operon protein C / Uncharacterized protein conserved in archaea (DUF2098) ...Methyl coenzyme M reductase system, component A2 / Methyl-coenzyme M reductase, protein C / Uncharacterised conserved protein UCP019164, methanogenesis / Uncharacterised protein family UPF0288, methanogenesis / Uncharacterised conserved protein UCP019464, methanogenesis / Uncharacterised conserved protein UCP037053 / Protein of unknown function DUF2098 / Methyl-coenzyme M reductase, protein C-like / Methyl-coenzyme M reductase operon protein C / Uncharacterized protein conserved in archaea (DUF2098) / Uncharacterized protein conserved in archaea (DUF2113) / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold / Methyl-coenzyme M reductase, alpha subunit, C-terminal / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2 / Methyl-coenzyme M reductase alpha subunit, C-terminal domain / Methyl-coenzyme M reductase alpha subunit, N-terminal domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 1-THIOETHANESULFONIC ACID / FACTOR 430 / FeFe cofactor / Chem-SHT / Coenzyme B / Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA / DUF2098 domain-containing protein / Methyl-coenzyme M reductase subunit alpha / Methyl-coenzyme M reductase subunit beta ...ADENOSINE-5'-TRIPHOSPHATE / 1-THIOETHANESULFONIC ACID / FACTOR 430 / FeFe cofactor / Chem-SHT / Coenzyme B / Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA / DUF2098 domain-containing protein / Methyl-coenzyme M reductase subunit alpha / Methyl-coenzyme M reductase subunit beta / Methyl-coenzyme M reductase subunit gamma / UPF0288 protein MmarC6_0796 / Methyl-coenzyme M reductase operon protein C / Methanogenesis marker protein 17 / Methanogenesis marker protein 7
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsRamirez-Amador, F. / Paul, S. / Kumar, A. / Schuller, J.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101075992European Union
CitationJournal: Nature / Year: 2025
Title: Structure of the ATP-driven methyl-coenzyme M reductase activation complex.
Authors: Fidel Ramírez-Amador / Sophia Paul / Anuj Kumar / Christian Lorent / Sebastian Keller / Stefan Bohn / Thinh Nguyen / Stefano Lometto / Dennis Vlegels / Jörg Kahnt / Darja Deobald / Frank ...Authors: Fidel Ramírez-Amador / Sophia Paul / Anuj Kumar / Christian Lorent / Sebastian Keller / Stefan Bohn / Thinh Nguyen / Stefano Lometto / Dennis Vlegels / Jörg Kahnt / Darja Deobald / Frank Abendroth / Olalla Vázquez / Georg Hochberg / Silvan Scheller / Sven T Stripp / Jan Michael Schuller /
Abstract: Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane. Its active site comprises coenzyme F, a porphyrin-based cofactor with a central nickel ion ...Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane. Its active site comprises coenzyme F, a porphyrin-based cofactor with a central nickel ion that is active exclusively in the Ni(I) state. How methanogenic archaea perform the reductive activation of F represents a major gap in our understanding of one of the most ancient bioenergetic systems in nature. Here we purified and characterized the MCR activation complex from Methanococcus maripaludis. McrC, a small subunit encoded in the mcr operon, co-purifies with the methanogenic marker proteins Mmp7, Mmp17, Mmp3 and the A2 component. We demonstrated that this complex can activate MCR in vitro in a strictly ATP-dependent manner, enabling the formation of methane. In addition, we determined the cryo-electron microscopy structure of the MCR activation complex exhibiting different functional states with local resolutions reaching 1.8-2.1 Å. Our data revealed three complex iron-sulfur clusters that formed an electron transfer pathway towards F. Topology and electron paramagnetic resonance spectroscopy analyses indicate that these clusters are similar to the [8Fe-9S-C] cluster, a maturation intermediate of the catalytic cofactor in nitrogenase. Altogether, our findings offer insights into the activation mechanism of MCR and prospects on the early evolution of nitrogenase.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Additional map / Part number: 4 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Additional map / Part number: 5 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Additional map / Part number: 6 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Additional map / Part number: 7 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Apr 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
J: UPF0288 protein MmarC6_0796
A: Methyl-coenzyme M reductase subunit gamma
B: Methyl-coenzyme M reductase subunit gamma
E: Methyl-coenzyme M reductase subunit beta
D: Methyl-coenzyme M reductase subunit beta
C: Methyl-coenzyme M reductase subunit alpha
F: Methyl-coenzyme M reductase subunit alpha
G: Methanogenesis marker protein 17
H: Methanogenesis marker protein 7
I: Methyl-coenzyme M reductase operon protein C
K: Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA
L: DUF2098 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)489,13125
Polymers482,98012
Non-polymers6,15113
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration, And mass photometry (not among options), mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 4 types, 4 molecules JIKL

#1: Protein UPF0288 protein MmarC6_0796 / Methanogenesis marker protein 3 / Mmp3


Mass: 56520.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Methanogenesis marker protein 3 / Source: (natural) Methanococcus maripaludis (archaea) / References: UniProt: A9A8E0
#7: Protein Methyl-coenzyme M reductase operon protein C


Mass: 24906.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Methyl-coenzyme M reductase subunit C / Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: GYY_08635 / Production host: Methanococcus maripaludis (archaea) / References: UniProt: G0H3B1
#8: Protein Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA / Methyl coenzyme M reductase system subunit A2


Mass: 59572.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Methyl-coenzyme M reductase system component A2 / Source: (natural) Methanococcus maripaludis (archaea) / References: UniProt: A0A2L1C9A1
#9: Protein DUF2098 domain-containing protein


Mass: 10640.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DUF2098 domain-containing protein / Source: (natural) Methanococcus maripaludis (archaea) / References: UniProt: A0A2L1CAX0

-
Methyl-coenzyme M reductase subunit ... , 3 types, 6 molecules ABEDCF

#2: Protein Methyl-coenzyme M reductase subunit gamma


Mass: 29665.488 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Methyl-coenzyme M reductase subunit gamma / Source: (natural) Methanococcus maripaludis (archaea)
References: UniProt: A0A2L1CBG2, coenzyme-B sulfoethylthiotransferase
#3: Protein Methyl-coenzyme M reductase subunit beta / Coenzyme-B sulfoethylthiotransferase beta


Mass: 46701.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Methyl-coenzyme M reductase subunit beta / Source: (natural) Methanococcus maripaludis (archaea)
References: UniProt: A0A2L1CBB3, coenzyme-B sulfoethylthiotransferase
#4: Protein Methyl-coenzyme M reductase subunit alpha


Mass: 61230.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Methyl-coenzyme M reductase subunit alpha / Source: (natural) Methanococcus maripaludis (archaea)
References: UniProt: A0A2L1CBB0, coenzyme-B sulfoethylthiotransferase

-
Methanogenesis marker protein ... , 2 types, 2 molecules GH

#5: Protein Methanogenesis marker protein 17 / Mmp17


Mass: 21119.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Methanogenesis marker protein 17 / Source: (natural) Methanococcus maripaludis (archaea) / References: UniProt: G0H411
#6: Protein Methanogenesis marker protein 7


Mass: 35024.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Methanogenesis marker protein / Source: (natural) Methanococcus maripaludis (archaea) / References: UniProt: Q6M050

-
Non-polymers , 8 types, 13 molecules

#10: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#11: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O3S2
#12: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22NO7PS
#13: Chemical ChemComp-SHT / O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE


Mass: 481.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H24NO10PS3 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-S5Q / FeFe cofactor


Mass: 747.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CFe8S9 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#16: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP
Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightValue: 0.5 MDa / Experimental value: YES
Source (natural)Organism: Methanococcus maripaludis (archaea)
Buffer solutionpH: 7.6
Buffer componentConc.: 20 mM / Name: HEPES / Formula: C8H18N2O4S
SpecimenConc.: 1.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Vitrification setup inside a Coy Lab's Vinyl anaerobic chamber to preserve the protein sample under strict anaerobic conditions (95% N2/ 5% H2)

-
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: 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) / Num. of real images: 28171
Details: Dataset obtained with 25 degree of pretilting to overcome preferred orientation issues

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv4particle selection
2cryoSPARCimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 944627
3D reconstructionResolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118247 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Details: Rigid body fitting in Chimera and Coot. Real-space refinement iterative rounds in Phenix.
Atomic model buildingSource name: AlphaFold / Type: in silico model

+
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