8Q4H | pdb_00008q4h

a membrane-bound menaquinol:organohalide oxidoreductase complex RDH complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Q4H

This is version 1.1 of the entry. See complete history

Literature

Structure of a membrane-bound menaquinol:organohalide oxidoreductase.

Cimmino, L.Duarte, A.G.Ni, D.Ekundayo, B.E.Pereira, I.A.C.Stahlberg, H.Holliger, C.Maillard, J.

(2023) Nat Commun 14: 7038-7038

  • DOI: https://doi.org/10.1038/s41467-023-42927-7
  • Primary Citation Related Structures: 
    8Q4H

  • PubMed Abstract: 

    Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohalides as substrates and contribute to energy conservation. Here, we present the structure of a menaquinol:organohalide oxidoreductase obtained by cryo-EM. The membrane-bound protein was isolated from Desulfitobacterium hafniense strain TCE1 as a PceA 2 B 2 complex catalysing the dechlorination of tetrachloroethene. Two catalytic PceA subunits are anchored to the membrane by two small integral membrane PceB subunits. The structure reveals two menaquinone molecules bound at the interface of the two different subunits, which are the starting point of a chain of redox cofactors for electron transfer to the active site. In this work, the structure elucidates how energy is conserved during organohalide respiration in menaquinone-dependent organohalide-respiring bacteria.


  • Organizational Affiliation
    • Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 139.08 kDa 
  • Atom Count: 9,694 
  • Modeled Residue Count: 1,184 
  • Deposited Residue Count: 1,184 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tetrachloroethene reductive dehalogenase
A, B
503Desulfitobacterium hafniense TCE1Mutation(s): 0 
EC: 1.21.99.5
Membrane Entity: Yes 
UniProt
Find proteins for Q8GJ31 (Desulfitobacterium hafniense)
Explore Q8GJ31 
Go to UniProtKB:  Q8GJ31
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GJ31
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable tetrachloroethene reductive dehalogenase membrane anchor protein
C, D
89Desulfitobacterium hafniense TCE1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8GJ30 (Desulfitobacterium hafniense)
Explore Q8GJ30 
Go to UniProtKB:  Q8GJ30
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GJ30
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COB

Query on COB



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
CO-METHYLCOBALAMIN
C63 H91 Co N13 O14 P
BMOGZGJBQIUQJG-BYLSPCLQSA-N
MQ7

Query on MQ7



Download:Ideal Coordinates CCD File
I [auth A],
N [auth B]
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
L [auth B],
M [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
JYF

Query on JYF



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
(~{Z})-1,2-bis(chloranyl)ethene
C2 H2 Cl2
KFUSEUYYWQURPO-UPHRSURJSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandCRSII5_177195
Swiss National Science FoundationSwitzerlandIZLCZ0_206089

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references