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- PDB-9qr3: Methyl-coenzyme M reductase of an ANME-2c from a microbial enrichment -

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Basic information

Entry
Database: PDB / ID: 9qr3
TitleMethyl-coenzyme M reductase of an ANME-2c from a microbial enrichment
Components
  • Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
  • Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
  • Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
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 / homology1-THIOETHANESULFONIC ACID / FACTOR 430 / : / Coenzyme B
Function and homology information
Biological speciesCandidatus Methanogasteraceae archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
B: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
C: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
D: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
E: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
F: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
G: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
H: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
I: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
J: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
K: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
L: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
M: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
N: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
O: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
P: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
Q: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
R: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
S: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
T: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
U: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
V: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
W: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
X: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,115,228120
Polymers1,099,41824
Non-polymers15,81196
Water176,7639812
1
A: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
B: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
C: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
D: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
E: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
F: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,09234
Polymers274,8546
Non-polymers4,23728
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59670 Å2
ΔGint-369 kcal/mol
Surface area57540 Å2
MethodPISA
2
G: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
H: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
I: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
J: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
K: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
L: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,97031
Polymers274,8546
Non-polymers4,11625
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59470 Å2
ΔGint-397 kcal/mol
Surface area57390 Å2
MethodPISA
3
M: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
N: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
O: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
P: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
Q: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
R: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,82730
Polymers274,8546
Non-polymers3,97224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58860 Å2
ΔGint-354 kcal/mol
Surface area57400 Å2
MethodPISA
4
S: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
T: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
U: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
V: Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c
W: Beta subunit of the Methyl-coenzyme M reductase from ANME-2c
X: Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,34025
Polymers274,8546
Non-polymers3,48619
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57970 Å2
ΔGint-349 kcal/mol
Surface area57590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.867, 157.456, 215.422
Angle α, β, γ (deg.)90.00, 90.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 24 molecules ADGJMPSVBEHKNQTWCFILORUX

#1: Protein
Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c


Mass: 61795.473 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: The alpha subunit contains seven post-translational modifications: Methylhistidine: 266 Methylarginine: 280 Methylglutamine: 410 Hydroxytryptophane: 437 Thioglycine: 455 Didehydroaspartate: ...Details: The alpha subunit contains seven post-translational modifications: Methylhistidine: 266 Methylarginine: 280 Methylglutamine: 410 Hydroxytryptophane: 437 Thioglycine: 455 Didehydroaspartate: 460 Methylcysteine: 462
Source: (natural) Candidatus Methanogasteraceae archaeon (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#2: Protein
Beta subunit of the Methyl-coenzyme M reductase from ANME-2c


Mass: 46238.676 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Candidatus Methanogasteraceae archaeon (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#3: Protein
Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c


Mass: 29393.064 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Candidatus Methanogasteraceae archaeon (archaea)
References: coenzyme-B sulfoethylthiotransferase

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Non-polymers , 10 types, 9908 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H51N6NiO13 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H22NO7PS / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#12: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9812 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.29 % / Description: Yellow rectangles/squares
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 ul protein at 24.6 g/l in 25 mM Tris/HCl pH 7.6, 10 % v/v glycerol, and 2 mM dithiothreitol was mixed with 2 ul crystallisation solution (30 % v/v 2-Methyl-2,4-pentanediol, 100 mM Tris pH ...Details: 2 ul protein at 24.6 g/l in 25 mM Tris/HCl pH 7.6, 10 % v/v glycerol, and 2 mM dithiothreitol was mixed with 2 ul crystallisation solution (30 % v/v 2-Methyl-2,4-pentanediol, 100 mM Tris pH 8.5, 500 mM NaCl, and 8% polyethylene glycol 8000) on a Junior Clover plate (Jena Bioscience). The reservoir contained 90 ul of crystallisation solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.34→127.16 Å / Num. obs: 1527343 / % possible obs: 96.2 % / Redundancy: 6.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.073 / Rrim(I) all: 0.183 / Net I/σ(I): 6.6
Reflection shellResolution: 1.34→1.5 Å / Redundancy: 6 % / Rmerge(I) obs: 1.671 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 76367 / CC1/2: 0.56 / Rpim(I) all: 0.737 / Rrim(I) all: 1.829 / % possible all: 66.6

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→98.93 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.45 / Stereochemistry target values: ML
Details: The model was built and corrected with COOT (Version 0.8.9.2) and refined with PHENIX.refine. All atoms were considered anisotropic, and hydrogens were added in riding mode. The model was ...Details: The model was built and corrected with COOT (Version 0.8.9.2) and refined with PHENIX.refine. All atoms were considered anisotropic, and hydrogens were added in riding mode. The model was validated by the MolProbity server (http://molprobity.biochem.duke.edu).
RfactorNum. reflection% reflection
Rfree0.1471 76552 5.01 %
Rwork0.1124 --
obs0.1142 1527210 66.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.77 Å2
Refinement stepCycle: LAST / Resolution: 1.34→98.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms76650 0 986 9812 87448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0180124
X-RAY DIFFRACTIONf_angle_d1.247108939
X-RAY DIFFRACTIONf_dihedral_angle_d14.29529757
X-RAY DIFFRACTIONf_chiral_restr0.08811837
X-RAY DIFFRACTIONf_plane_restr0.01614394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.2451240.2025333X-RAY DIFFRACTION0
1.36-1.380.2065950.2031821X-RAY DIFFRACTION3
1.38-1.390.2711640.20553049X-RAY DIFFRACTION4
1.39-1.410.24782350.22184918X-RAY DIFFRACTION7
1.41-1.430.26134040.22117730X-RAY DIFFRACTION11
1.43-1.450.24925900.212211066X-RAY DIFFRACTION15
1.45-1.470.24948110.211316121X-RAY DIFFRACTION22
1.47-1.490.260110810.203622582X-RAY DIFFRACTION31
1.49-1.510.243114460.205329030X-RAY DIFFRACTION40
1.51-1.540.237717970.200835223X-RAY DIFFRACTION48
1.54-1.570.22421260.190439894X-RAY DIFFRACTION55
1.57-1.590.230923240.182843974X-RAY DIFFRACTION60
1.59-1.630.222225110.165848074X-RAY DIFFRACTION66
1.63-1.660.211326620.160852603X-RAY DIFFRACTION72
1.66-1.690.200929720.152557235X-RAY DIFFRACTION78
1.69-1.730.203432090.150862098X-RAY DIFFRACTION85
1.73-1.780.199435760.141666094X-RAY DIFFRACTION91
1.78-1.830.1936760.136671598X-RAY DIFFRACTION98
1.83-1.880.168536940.123773022X-RAY DIFFRACTION100
1.88-1.940.164638000.117773071X-RAY DIFFRACTION100
1.94-2.010.149839690.102872849X-RAY DIFFRACTION100
2.01-2.090.141838110.094772983X-RAY DIFFRACTION100
2.09-2.180.130438920.089473051X-RAY DIFFRACTION100
2.18-2.30.127341090.085472742X-RAY DIFFRACTION100
2.3-2.440.12439250.087573047X-RAY DIFFRACTION100
2.44-2.630.125538470.09373107X-RAY DIFFRACTION100
2.63-2.90.12540140.098772995X-RAY DIFFRACTION100
2.9-3.320.128639850.102473142X-RAY DIFFRACTION100
3.32-4.180.114339030.090973322X-RAY DIFFRACTION100
4.18-98.930.13139000.116973884X-RAY DIFFRACTION100

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