Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2BC Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2BC 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 432.50 kDa 
• Atom Count: 32144 
• Residue Count: 3861 
• Unique protein chains: 3

3SQG

Crystal structure of a methyl-coenzyme M reductase purified from Black Sea mats

• DOI: 10.2210/pdb3SQG/pdb

• Classification: TRANSFERASE
• Organism(s): uncultured archaeon
• Mutation(s): No 


• Deposited: 2011-07-05 Released: 2011-11-30 
• Deposition Author(s): Shima, S., Krueger, M., Weinert, T., Demmer, U., Thauer, R.K., Ermler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.206 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Literature

Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically.

Shima, S., Krueger, M., Weinert, T., Demmer, U., Kahnt, J., Thauer, R.K., Ermler, U.

(2011) Nature 481: 98-101

• PubMed: 22121022 
• DOI: 10.1038/nature10663
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The anaerobic oxidation of methane (AOM) with sulphate, an area currently generating great interest in microbiology, is accomplished by consortia of methanotrophic archaea (ANME) and sulphate-reducing bacteria. The enzyme activating methane in methanotrophic archaea has tentatively been identified as a homologue of methyl-coenzyme M reductase (MCR) that catalyses the methane-forming step in methanogenic archaea. Here we report an X-ray structure of the 280 kDa heterohexameric ANME-1 MCR complex. It was crystallized uniquely from a protein ensemble purified from consortia of microorganisms collected with a submersible from a Black Sea mat catalysing AOM with sulphate. Crystals grown from the heterogeneous sample diffract to 2.1 Å resolution and consist of a single ANME-1 MCR population, demonstrating the strong selective power of crystallization. The structure revealed ANME-1 MCR in complex with coenzyme M and coenzyme B, indicating the same substrates for MCR from methanotrophic and methanogenic archaea. Differences between the highly similar structures of ANME-1 MCR and methanogenic MCR include a F(430) modification, a cysteine-rich patch and an altered post-translational amino acid modification pattern, which may tune the enzymes for their functions in different biological contexts.

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Organizational Affiliation: 

Max Planck Institute for Terrestrial Microbiology, Karl-Frisch-Strasse 10, D-35043 Marburg, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Methyl coenzyme M reductase, alpha subunit	A, D, G	579	uncultured archaeon	Mutation(s): 0  Gene Names: mcrA, BSM_29630 EC: 2.8.4.1
Find proteins for D1JBK4 (uncultured archaeon) Explore D1JBK4  Go to UniProtKB:  D1JBK4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Methyl-coenzyme M reductase, beta subunit	B, E, H	433	uncultured archaeon	Mutation(s): 0  Gene Names: mcrB, BSM_29610 EC: 2.8.4.1
Find proteins for D1JBK2 (uncultured archaeon) Explore D1JBK2  Go to UniProtKB:  D1JBK2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Methyl-coenzyme M reductase, gamma subunit	C, F, I	279	uncultured archaeon	Mutation(s): 0  Gene Names: mcrG, BSM_29620 EC: 2.8.4.1
Find proteins for D1JBK3 (uncultured archaeon) Explore D1JBK3  Go to UniProtKB:  D1JBK3

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M43	A, D, G	(17[2]S)-17[2]-methylthio-coenzyme F43 C43 H53 N6 Ni O13 S UOYNURPVGLQPFO-AEEVBHTRSA-M
TP7	A, G	Coenzyme B C11 H22 N O7 P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N
P6G	B	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE	A, D, E, F, G, H	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	A, D, G	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
COM	A, D, G	1-THIOETHANESULFONIC ACID C2 H6 O3 S2 ZNEWHQLOPFWXOF-UHFFFAOYSA-N
SO4	A, B, C, D, H, I	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C, E	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, G	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0AF	A,D,G	L-PEPTIDE LINKING	C11 H12 N2 O3		TRP
GL3	A,D,G	L-PEPTIDE LINKING	C2 H5 N O S		GLY
MHO	A,D,G	L-PEPTIDE LINKING	C5 H11 N O3 S		MET
MHS	A,D,G	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.206 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.86	α = 90
b = 412.49	β = 90
c = 165.51	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-05 
• Released Date: 2011-11-30 
Deposition Author(s): Shima, S., Krueger, M., Weinert, T., Demmer, U., Thauer, R.K., Ermler, U.

Revision History 

• Version 1.0: 2011-11-30
  Type: Initial release
  
• Version 1.1: 2011-12-28
  Changes: Database references
• Version 1.2: 2012-01-04
  Changes: Database references
• Version 1.3: 2015-05-20
  Changes: Non-polymer description
• Version 1.4: 2015-05-27
  Changes: Other
• Version 1.5: 2017-11-08
  Changes: Refinement description