[English] 日本語
Yorodumi
- PDB-9qr1: Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qr1
TitleMethyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens sp. BLZ2 from a bioreactor enrichment culture
Components
  • (Methyl-coenzyme M reductase subunit ...) x 2
  • coenzyme-B sulfoethylthiotransferase
KeywordsTRANSFERASE / methanotrophy / anaerobic methanotrophic archaea / methane oxidation / ANME / methyl-coenzyme M reductase / MCR / reverse methanogenesis / nickel-dependent enzyme / coenzyme M / coenzyme B / F430 cofactor
Function / homology
Function and homology information


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding
Similarity search - Function
Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / 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 beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain ...Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / 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 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
Similarity search - Domain/homology
1-THIOETHANESULFONIC ACID / FACTOR 430 / : / NITRATE ION / Coenzyme B / coenzyme-B sulfoethylthiotransferase / Methyl-coenzyme M reductase subunit alpha / Methyl-coenzyme M reductase subunit beta
Similarity search - Component
Biological speciesCandidatus Methanoperedens sp. BLZ2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsMueller, M.-C. / Wagner, T.
Funding supportEuropean Union, Germany, Netherlands, 5items
OrganizationGrant numberCountry
European Research Council (ERC)101125699European Union
German Research Foundation (DFG)WA 4053/1-1 Germany
Netherlands Organisation for Scientific Research (NWO)VI.Vidi.223.012 Netherlands
Netherlands Organisation for Scientific Research (NWO)024.002.002 Netherlands
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2025
Title: Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications.
Authors: Muller, M.C. / Wissink, M. / Mukherjee, P. / Von Possel, N. / Laso-Perez, R. / Engilberge, S. / Carpentier, P. / Kahnt, J. / Wegener, G. / Welte, C.U. / Wagner, T.
History
DepositionApr 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-coenzyme M reductase subunit alpha
B: Methyl-coenzyme M reductase subunit beta
C: coenzyme-B sulfoethylthiotransferase
D: Methyl-coenzyme M reductase subunit alpha
E: Methyl-coenzyme M reductase subunit beta
F: coenzyme-B sulfoethylthiotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,69941
Polymers270,2006
Non-polymers4,49935
Water61,5933419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: All other methyl-coenyzme M reductase models follow the same organization.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60960 Å2
ΔGint-194 kcal/mol
Surface area58080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.575, 189.299, 84.109
Angle α, β, γ (deg.)90.00, 114.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Methyl-coenzyme M reductase subunit ... , 2 types, 4 molecules ADBE

#1: Protein Methyl-coenzyme M reductase subunit alpha / Alpha subunit of the Methyl-Coenzyme M reductase


Mass: 61535.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The alpha subunit contains six post-translational modifications: Methylhistidine 268 Methylarginine 282 Hydroxytryptophane 439 Thioglycine 457 Didehydroaspartate 462 Methylcysteine 464
Source: (natural) Candidatus Methanoperedens sp. BLZ2 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: BLZ2 / Tissue: /
References: UniProt: A0A6A2FLY3, coenzyme-B sulfoethylthiotransferase
#2: Protein Methyl-coenzyme M reductase subunit beta / Coenzyme-B sulfoethylthiotransferase beta / Beta subunit of the Methyl-Coenzyme M reductase


Mass: 45366.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Methanoperedens sp. BLZ2 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: BLZ2 / Tissue: /
References: UniProt: A0A6A2G3Q8, coenzyme-B sulfoethylthiotransferase

-
Protein , 1 types, 2 molecules CF

#3: Protein coenzyme-B sulfoethylthiotransferase / Gamma subunit of the Methyl-Coenzyme M reductase


Mass: 28197.822 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The gamma subunit contains a methylhistidine at position 159.
Source: (natural) Candidatus Methanoperedens sp. BLZ2 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: BLZ2 / Tissue: /
References: UniProt: A0A5E4HJB0, coenzyme-B sulfoethylthiotransferase

-
Non-polymers , 8 types, 3454 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3419 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: Thick, yellow, brick-shaped
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystallisation was carried out on a junior Clover plate using a solution containing 20% w/v polyethylene glycol 3,350, 50 mM Tris pH 8.0, and 200 mM potassium nitrate. The reservoir ...Details: Crystallisation was carried out on a junior Clover plate using a solution containing 20% w/v polyethylene glycol 3,350, 50 mM Tris pH 8.0, and 200 mM potassium nitrate. The reservoir contained 100 ul of crystallisation solution. 5 ul protein at 2.19 mg/ml in 25 mM Tris/HCl pH 8.0, 100 mM NaCl, 10% v/v glycerol and 2 mM dithiothreitol were mixed with 2 ul of the crystallisation solution. Crystals were soaked in a crystallisation solution supplemented with 20% ethylene glycol before freezing in liquid nitrogen.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 0.976→76.674 Å / Num. obs: 1130261 / % possible obs: 96.5 % / Redundancy: 7.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.045 / Rrim(I) all: 0.128 / Net I/σ(I): 9.4
Reflection shellResolution: 0.976→1.04 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 56513 / CC1/2: 0.667 / Rpim(I) all: 0.468 / Rrim(I) all: 1.26 / % possible all: 70.9

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→41.78 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.72 / Stereochemistry target values: ML
Details: The model was built and corrected with COOT (Version 0.8.9.2)(52) and refined with PHENIX.refine. All atoms were considered anisotropic, with hydrogens added in riding mode. The model was ...Details: The model was built and corrected with COOT (Version 0.8.9.2)(52) and refined with PHENIX.refine. All atoms were considered anisotropic, with hydrogens added in riding mode. The model was validated by the MolProbity server (http://molprobity.biochem.duke.edu).
RfactorNum. reflection% reflection
Rfree0.1176 57217 5.06 %
Rwork0.1025 --
obs0.1033 1130120 84.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.72 Å2
Refinement stepCycle: LAST / Resolution: 0.98→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18876 0 287 3419 22582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0120432
X-RAY DIFFRACTIONf_angle_d1.34127855
X-RAY DIFFRACTIONf_dihedral_angle_d14.0757751
X-RAY DIFFRACTIONf_chiral_restr0.0993045
X-RAY DIFFRACTIONf_plane_restr0.0163680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.990.28491940.25753075X-RAY DIFFRACTION7
0.99-10.24422250.24865013X-RAY DIFFRACTION12
1-1.010.24073780.24037892X-RAY DIFFRACTION19
1.01-1.020.25945680.234412933X-RAY DIFFRACTION30
1.02-1.040.252811050.226419914X-RAY DIFFRACTION47
1.04-1.050.243814490.222326457X-RAY DIFFRACTION63
1.05-1.070.222416220.201531307X-RAY DIFFRACTION74
1.07-1.080.198619420.187836791X-RAY DIFFRACTION87
1.08-1.10.18921020.169740507X-RAY DIFFRACTION96
1.1-1.120.177421510.157941701X-RAY DIFFRACTION98
1.12-1.140.158522490.143342284X-RAY DIFFRACTION100
1.14-1.160.150322870.132542215X-RAY DIFFRACTION100
1.16-1.180.147522940.126342309X-RAY DIFFRACTION100
1.18-1.20.13522060.11842409X-RAY DIFFRACTION100
1.2-1.230.131522190.109242353X-RAY DIFFRACTION100
1.23-1.260.13122410.107142359X-RAY DIFFRACTION100
1.26-1.290.115822700.095142310X-RAY DIFFRACTION100
1.29-1.320.113123390.089242297X-RAY DIFFRACTION100
1.32-1.360.104324120.084942289X-RAY DIFFRACTION100
1.36-1.410.109823730.083242202X-RAY DIFFRACTION100
1.41-1.460.099422390.078842368X-RAY DIFFRACTION100
1.46-1.520.093520580.074342576X-RAY DIFFRACTION100
1.52-1.590.09221990.075142472X-RAY DIFFRACTION100
1.59-1.670.094821750.078542476X-RAY DIFFRACTION100
1.67-1.770.097723060.082742341X-RAY DIFFRACTION100
1.77-1.910.099923200.087942405X-RAY DIFFRACTION100
1.91-2.10.096822790.087242397X-RAY DIFFRACTION100
2.1-2.410.095122140.084742510X-RAY DIFFRACTION100
2.41-3.030.106622660.095942454X-RAY DIFFRACTION100
3.03-41.780.115825350.105142287X-RAY DIFFRACTION100

+
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