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- EMDB-18148: a membrane-bound menaquinol:organohalide oxidoreductase complex R... -

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Basic information

Entry
Database: EMDB / ID: EMD-18148
Titlea membrane-bound menaquinol:organohalide oxidoreductase complex RDH complex
Map data
Sample
  • Complex: a membrane-bound menaquinol:organohalide oxidoreductase
    • Protein or peptide: Probable tetrachloroethene reductive dehalogenase membrane anchor protein
  • Protein or peptide: Tetrachloroethene reductive dehalogenase
  • Ligand: (~{Z})-1,2-bis(chloranyl)ethene
  • Ligand: CO-METHYLCOBALAMIN
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: MENAQUINONE-7
  • Ligand: water
KeywordsRDH menaquinol:organohalide oxidoreductase / ELECTRON TRANSPORT
Function / homology
Function and homology information


tetrachloroethene reductive dehalogenase / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / plasma membrane
Similarity search - Function
TAT (twin-arginine translocation) pathway signal sequence / 4Fe-4S double cluster binding domain / Reductive dehalogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Probable tetrachloroethene reductive dehalogenase membrane anchor protein / Tetrachloroethene reductive dehalogenase
Similarity search - Component
Biological speciesDesulfitobacterium hafniense TCE1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsDongchun N / Ekundayo B / Henning S / Julien M / Holliger C / Cimmino L
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_177195 Switzerland
Swiss National Science FoundationIZLCZ0_206089 Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: Structure of a membrane-bound menaquinol:organohalide oxidoreductase.
Authors: Lorenzo Cimmino / Américo G Duarte / Dongchun Ni / Babatunde E Ekundayo / Inês A C Pereira / Henning Stahlberg / Christof Holliger / Julien Maillard /
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 ...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 PceAB 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.
History
DepositionAug 7, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18148.png

Downloads & links

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Map

FileDownload / File: emd_18148.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 300 pix.
= 204. Å		0.68 Å/pix.
x 300 pix.
= 204. Å		0.68 Å/pix.
x 300 pix.
= 204. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.5514069 - 0.74166846
Average (Standard dev.)0.00042886008 (±0.0252677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18148_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18148_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : a membrane-bound menaquinol:organohalide oxidoreductase

EntireName: a membrane-bound menaquinol:organohalide oxidoreductase
Components
  • Complex: a membrane-bound menaquinol:organohalide oxidoreductase
    • Protein or peptide: Probable tetrachloroethene reductive dehalogenase membrane anchor protein
  • Protein or peptide: Tetrachloroethene reductive dehalogenase
  • Ligand: (~{Z})-1,2-bis(chloranyl)ethene
  • Ligand: CO-METHYLCOBALAMIN
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: MENAQUINONE-7
  • Ligand: water

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Supramolecule #1: a membrane-bound menaquinol:organohalide oxidoreductase

SupramoleculeName: a membrane-bound menaquinol:organohalide oxidoreductase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 / Details: PceA2B2
Source (natural)Organism: Desulfitobacterium hafniense TCE1 (bacteria)
Molecular weightTheoretical: 130 kDa/nm

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Macromolecule #1: Tetrachloroethene reductive dehalogenase

MacromoleculeName: Tetrachloroethene reductive dehalogenase / type: protein_or_peptide / ID: 1 / Details: (COB)(SF4)(SF4)(MQ7) / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Desulfitobacterium hafniense TCE1 (bacteria)
Molecular weightTheoretical: 56.620824 KDa
SequenceString: TSEFPYKVDA KYQRYNSLKN FFEKTFDPEA NKTPIKFHYD DVSKITGKKD TGKDLPTLNA ERLGIKGRPA THTETSILFH TQHLGAMLT QRHNETGWTG LDEALNAGAW AVEFDYSGFN ATGGGPGSVI PLYPINPMTN EIANEPVMVP GLYNWDNIDV E SVRQQGQQ ...String:
TSEFPYKVDA KYQRYNSLKN FFEKTFDPEA NKTPIKFHYD DVSKITGKKD TGKDLPTLNA ERLGIKGRPA THTETSILFH TQHLGAMLT QRHNETGWTG LDEALNAGAW AVEFDYSGFN ATGGGPGSVI PLYPINPMTN EIANEPVMVP GLYNWDNIDV E SVRQQGQQ WKFESKEEAS KIVKKATRLL GADLVGIAPY DERWTYSTWG RKIYKPCKMP NGRTKYLPWD LPKMLSGGGV EV FGHAKFE PDWEKYAGFK PKSVIVFVLE EDYEAIRTSP SVISSATVGK SYSNMAEVAY KIAVFLRKLG YYAAPCGNDT GIS VPMAVQ AGLGEAGRNG LLITQKFGPR HRIAKVYTDL ELAPDKPRKF GVREFCRLCK KCADACPAQA ISHEKDPKVL QPED CEVAE NPYTEKWHLD SNRCGSFWAY NGSPCSNCVA VCSWNKVETW NHDVARIATQ IPLLQDAARK FDEWFGYNGP VNPDE RLES GYVQNMVKDF WNNPESIKQ

UniProtKB: Tetrachloroethene reductive dehalogenase

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Macromolecule #2: Probable tetrachloroethene reductive dehalogenase membrane anchor...

MacromoleculeName: Probable tetrachloroethene reductive dehalogenase membrane anchor protein
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Desulfitobacterium hafniense TCE1 (bacteria)
Molecular weightTheoretical: 10.126991 KDa
SequenceString:
MNIYDVLIWM ALGMTALLIQ YGIWRYLKGK GKDTIPLQIC GFLANFFFIF ALAWGYSSFS EREYQAIGMG FIFFGGTALI PAIITYRLA

UniProtKB: Probable tetrachloroethene reductive dehalogenase membrane anchor protein

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Macromolecule #3: (~{Z})-1,2-bis(chloranyl)ethene

MacromoleculeName: (~{Z})-1,2-bis(chloranyl)ethene / type: ligand / ID: 3 / Number of copies: 2 / Formula: JYF
Molecular weightTheoretical: 96.943 Da
Chemical component information

ChemComp-JYF:
(~{Z})-1,2-bis(chloranyl)ethene

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Macromolecule #4: CO-METHYLCOBALAMIN

MacromoleculeName: CO-METHYLCOBALAMIN / type: ligand / ID: 4 / Number of copies: 2 / Formula: COB
Molecular weightTheoretical: 1.344382 KDa
Chemical component information

ChemComp-COB:
CO-METHYLCOBALAMIN

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 4 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #6: MENAQUINONE-7

MacromoleculeName: MENAQUINONE-7 / type: ligand / ID: 6 / Number of copies: 2 / Formula: MQ7
Molecular weightTheoretical: 648.999 Da
Chemical component information

ChemComp-MQ7:
MENAQUINONE-7

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 14 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34078
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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