9QQT | pdb_00009qqt

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture

PDB DOI: https://doi.org/10.2210/pdb9QQT/pdb

Classification: TRANSFERASE
Organism(s): Candidatus Methanoperedens sp.
Mutation(s): No

Deposited: 2025-04-02 Released: 2025-07-23
Deposition Author(s): Mueller, M.-C., Wagner, T.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG), Netherlands Organisation for Scientific Research (NWO), Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free:
0.148 (Depositor), 0.164 (DCC)
R-Value Work:
0.128 (Depositor), 0.153 (DCC)
R-Value Observed:
0.129 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications

Mueller, 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.

To be published.

Macromolecule Content

Total Structure Weight: 276.06 kDa
Atom Count: 23,324
Modeled Residue Count: 2,489
Deposited Residue Count: 2,498
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit alpha	A	566	Candidatus Methanoperedens sp.	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A822J3V5 (Methanosarcinales archaeon) Explore A0A822J3V5 Go to UniProtKB: A0A822J3V5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A822J3V5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit beta	B, E	434	Candidatus Methanoperedens sp.	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A822J4Y5 (Methanosarcinales archaeon) Explore A0A822J4Y5 Go to UniProtKB: A0A822J4Y5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A822J4Y5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit gamma	C, F	249	Candidatus Methanoperedens sp.	Mutation(s): 0 EC: 2.8.4.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit alpha	D	566	Candidatus Methanoperedens sp.	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A822J3V5 (Methanosarcinales archaeon) Explore A0A822J3V5 Go to UniProtKB: A0A822J3V5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A822J3V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 (Subject of Investigation/LOI) Query on F43 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain H [auth A] mmCIF format, chain Z [auth D]	H [auth A], Z [auth D]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain H [auth A] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain Z [auth D]
SHT (Subject of Investigation/LOI) Query on SHT Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain N [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain N [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain N [auth A]	GA [auth D], N [auth A]	O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE C₁₃ H₂₄ N O₁₀ P S₃ CVQZOMWKHKTFCZ-UIALCFJWSA-N		Interactions Focus chain GA [auth D] Focus chain N [auth A] Interactions & Density Focus chain GA [auth D] Focus chain N [auth A]
TP7 (Subject of Investigation/LOI) Query on TP7 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain J [auth A]	AA [auth D], J [auth A]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A]
COM (Subject of Investigation/LOI) Query on COM Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain X [auth D] MOL2 format, chain M [auth A] MOL2 format, chain X [auth D] mmCIF format, chain M [auth A] mmCIF format, chain X [auth D]	M [auth A], X [auth D]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain X [auth D] Interactions & Density Focus chain M [auth A] Focus chain X [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth D]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], HA [auth D], I [auth A], IA [auth E], JA [auth E], K [auth A], KA [auth F], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth C], W [auth C], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Modified Residues 8 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM Query on AGM	A	L-PEPTIDE LINKING	C₇ H₁₇ N₄ O₂		ARG
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
DYA Query on DYA	A	L-PEPTIDE LINKING	C₄ H₅ N O₄		ASP
GL3 Query on GL3	A	L-PEPTIDE LINKING	C₂ H₅ N O S		GLY
MHS Query on MHS	A	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
SMC Query on SMC	A	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS
TRX Query on TRX	A	L-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₃		TRP
A1I9G Query on A1I9G	C, F	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free: 0.148 (Depositor), 0.164 (DCC)
R-Value Work: 0.128 (Depositor), 0.153 (DCC)
R-Value Observed: 0.129 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.621	α = 90
b = 189.823	β = 114.36
c = 83.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Mueller, M.-C.

Wagner, T.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101125699
German Research Foundation (DFG)	Germany	WA 4053/1-1
Netherlands Organisation for Scientific Research (NWO)	Netherlands	VI.Vidi.223.012
Netherlands Organisation for Scientific Research (NWO)	Netherlands	024.002.002
Max Planck Society	Germany	--