3SQG | pdb_00003sqg

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.206 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/nature10663
  • Primary Citation Related Structures: 
    3SQG

  • 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.


  • Organizational Affiliation
    • Max Planck Institute for Terrestrial Microbiology, Karl-Frisch-Strasse 10, D-35043 Marburg, Germany. shima@mpi-marburg.mpg.de

Macromolecule Content 

  • Total Structure Weight: 432.5 kDa 
  • Atom Count: 32,144 
  • Modeled Residue Count: 3,861 
  • Deposited Residue Count: 3,873 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methyl coenzyme M reductase, alpha subunit
A, D, G
579uncultured archaeonMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for A0ACD6B9H7 (Uncultured archaeon)
Explore A0ACD6B9H7 
Go to UniProtKB:  A0ACD6B9H7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9H7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Methyl-coenzyme M reductase, beta subunit
B, E, H
433uncultured archaeonMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for A0ACD6B9H5 (Uncultured archaeon)
Explore A0ACD6B9H5 
Go to UniProtKB:  A0ACD6B9H5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9H5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Methyl-coenzyme M reductase, gamma subunit
C, F, I
279uncultured archaeonMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for A0ACD6B9H6 (Uncultured archaeon)
Explore A0ACD6B9H6 
Go to UniProtKB:  A0ACD6B9H6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9H6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M43

Query on M43



Download:Ideal Coordinates CCD File
JA [auth G],
L [auth A],
Z [auth D]
(17[2]S)-17[2]-methylthio-coenzyme F43
C43 H53 N6 Ni O13 S
UOYNURPVGLQPFO-AEEVBHTRSA-M
TP7

Query on TP7



Download:Ideal Coordinates CCD File
J [auth A],
KA [auth G],
M [auth A]
Coenzyme B
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
U [auth B]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
BA [auth D]
GA [auth E]
IA [auth F]
MA [auth G]
N [auth A]
BA [auth D],
GA [auth E],
IA [auth F],
MA [auth G],
N [auth A],
QA [auth H]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
CA [auth D]
DA [auth D]
NA [auth G]
O [auth A]
OA [auth G]
CA [auth D],
DA [auth D],
NA [auth G],
O [auth A],
OA [auth G],
P [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
COM

Query on COM



Download:Ideal Coordinates CCD File
AA [auth D],
K [auth A],
LA [auth G]
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
EA [auth D]
FA [auth D]
Q [auth A]
R [auth A]
RA [auth H]
EA [auth D],
FA [auth D],
Q [auth A],
R [auth A],
RA [auth H],
SA [auth I],
V [auth B],
W [auth B],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
HA [auth E],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
PA [auth G],
T [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
S [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
0AF
Query on 0AF
A, D, G
L-PEPTIDE LINKINGC11 H12 N2 O3TRP
GL3
Query on GL3
A, D, G
L-PEPTIDE LINKINGC2 H5 N O SGLY
MHO
Query on MHO
A, D, G
L-PEPTIDE LINKINGC5 H11 N O3 SMET
MHS
Query on MHS
A, D, G
L-PEPTIDE LINKINGC7 H11 N3 O2HIS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.206 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.86α = 90
b = 412.49β = 90
c = 165.51γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.6: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary