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- EMDB-25879: Cryo-EM of the OmcE nanowires from Geobacter sulfurreducens -

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Basic information

Entry
Database: EMDB / ID: EMD-25879
TitleCryo-EM of the OmcE nanowires from Geobacter sulfurreducens
Map dataCryo-EM of the OmcE nanowires from Geobacter sulfurreducens
Sample
  • Complex: Filament of OmcE protein
    • Protein or peptide: Cytochrome c
  • Ligand: HEME C
Keywordshelical symmetry / cytochrome nanowire / filament / ELECTRON TRANSPORT / PROTEIN FIBRIL
Function / homologyDoubled CXXCH motif / Doubled CXXCH motif (Paired_CXXCH_1) / Multiheme cytochrome superfamily / Cytochrome c
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang F / Mustafa K
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Nat Microbiol / Year: 2022
Title: Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing.
Authors: Fengbin Wang / Khawla Mustafa / Victor Suciu / Komal Joshi / Chi H Chan / Sol Choi / Zhangli Su / Dong Si / Allon I Hochbaum / Edward H Egelman / Daniel R Bond /
Abstract: Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were ...Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
History
DepositionJan 7, 2022-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25879.png

Downloads & links

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Map

FileDownload / File: emd_25879.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of the OmcE nanowires from Geobacter sulfurreducens
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.8417124 - 1.2025987
Average (Standard dev.)0.00075723877 (±0.016689895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Filament of OmcE protein

EntireName: Filament of OmcE protein
Components
  • Complex: Filament of OmcE protein
    • Protein or peptide: Cytochrome c
  • Ligand: HEME C

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Supramolecule #1: Filament of OmcE protein

SupramoleculeName: Filament of OmcE protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA

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Macromolecule #1: Cytochrome c

MacromoleculeName: Cytochrome c / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA
Molecular weightTheoretical: 23.839742 KDa
SequenceString: MRSEVKIGLA LTALLVAVTA AGAASIKNTK HDLSSGSTGA TFKATNTDQI CVFCHTPHNA QQDIPLWNRG NPTASTFTLY SSSSMNNVP VKQGFTADSI SLFCMSCHDG ATGLGGAVHN DPNGAAIAMV GGNDLITGEA NLGTDLSNDH PVNFEVTPAG I AADGNLGA ...String:
MRSEVKIGLA LTALLVAVTA AGAASIKNTK HDLSSGSTGA TFKATNTDQI CVFCHTPHNA QQDIPLWNRG NPTASTFTLY SSSSMNNVP VKQGFTADSI SLFCMSCHDG ATGLGGAVHN DPNGAAIAMV GGNDLITGEA NLGTDLSNDH PVNFEVTPAG I AADGNLGA LDTGTNPPTM KTGDVTNGLP LFKSARGATT LECGSCHKVH DNTDAPFLRT TMAGSKLCLG CHKK

UniProtKB: Cytochrome c

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Macromolecule #2: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 2 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 33.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 58.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 346826
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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