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- EMDB-73506: A Bundled Antiparallel Cytochrome Nanowire Produced by Desulfurom... -

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Basic information

Entry
Database: EMDB / ID: EMD-73506
TitleA Bundled Antiparallel Cytochrome Nanowire Produced by Desulfuromonas soudanensis WTL
Map data
Sample
  • Complex: Multi-heme cytochrome nanowire
    • Protein or peptide: Putative multiheme cytochrome c
  • Ligand: HEME C
  • Ligand: CALCIUM ION
Keywordsmulti-heme cytochrome / nanowire / EET / cryo-EM / ELECTRON TRANSPORT
Function / homologyDoubled CXXCH motif / Doubled CXXCH motif (Paired_CXXCH_1) / Multiheme cytochrome superfamily / Putative multiheme cytochrome c
Function and homology information
Biological speciesDesulfuromonas soudanensis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsPetersen HA / Chan CH / Bond DR / Wang F
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)SC0024303 United States
CitationJournal: mBio / Year: 2026
Title: A bundled anti-parallel cytochrome nanowire structure suggests roles in cell-cell electron transfer and biofilm formation.
Authors: Holly A Petersen / Chi H Chan / Gilbert O Carpenter / Media Zakizadeh Tabari / Jessie Lynda Fields / Ayisha Zia / Shane T Rich-New / Allon I Hochbaum / Daniel R Bond / Fengbin Wang /
Abstract: Long-range extracellular electron transfer enables respiring microbes to use minerals, organisms, or electrodes as electron acceptors by transporting electrons microns away from the cell surface. ...Long-range extracellular electron transfer enables respiring microbes to use minerals, organisms, or electrodes as electron acceptors by transporting electrons microns away from the cell surface. This process is primarily studied in , which produces at least three distinct, micrometer-long, multiheme cytochrome nanowires capable of electron transfer. However, the distribution and higher-order structure of such nanowires remains largely unknown. Here, we employed cryo-electron microscopy to determine the atomic structure of a unique cytochrome nanowire from WTL, a halophilic, iron- and electrode-reducing bacterium from deep subsurface brine. These filaments are based on an OmcE tetraheme cytochrome homolog that assembles into highly ordered bundles of anti-parallel filaments. Electronic measurements of purified nanowire bundle films reveal that these bundles are conductive, with conductance increasing in a concentration-dependent manner. The apparent midpoint potential of these OmcE bundles was -145 mV vs SHE. They exhibit redox activity over a ~370 mV window attributable to five electrostatically coupled hemes, suggesting heme-heme interaction beyond the boundaries of individual OmcE repeat units. Observations of these bundles under diverse buffer conditions suggest that they represent stable supramolecular assemblies, although direct confirmation within intact biofilms remains a future goal. Furthermore, a similar cytochrome bundle structure was observed in , showing that this quaternary structure may be a common feature among nanowires secreted by electroactive microbes. Our findings demonstrate that cytochrome nanowires are widespread and can form specialized bundle interfaces. This novel state could facilitate conductive biofilm formation and form the basis for direct microbial electron exchange.All available structures of filaments containing a central core of closely spaced multiheme c-type cytochromes are derived from only a few organisms and are based on individual fibers easily imaged by cryo-electron microscopy. While imaging enriched preparations of extracellular appendages from a bacterium isolated from deep subsurface brine, we observed ordered bundles of anti-parallel cytochrome filaments. This quaternary arrangement contained specific contacts between adjacent nanowires, and a similar structure could be found in a relative from a related genus. This first report of bundling by nanowires suggests that such conductive structures may be missed in traditional surveys searching for novel filaments and provides an explanation for how nanowires could directly link adjacent cells in biofilms and granular communities.
History
DepositionOct 22, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_73506.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å
1.07 Å/pix.
x 320 pix.
= 342.4 Å
1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0486
Minimum - Maximum-0.0018049523 - 2.195223
Average (Standard dev.)0.0029335597 (±0.037971966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73506_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_73506_half_map_2.map
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Sample components

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Entire : Multi-heme cytochrome nanowire

EntireName: Multi-heme cytochrome nanowire
Components
  • Complex: Multi-heme cytochrome nanowire
    • Protein or peptide: Putative multiheme cytochrome c
  • Ligand: HEME C
  • Ligand: CALCIUM ION

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Supramolecule #1: Multi-heme cytochrome nanowire

SupramoleculeName: Multi-heme cytochrome nanowire / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Desulfuromonas soudanensis (bacteria) / Strain: WTL

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Macromolecule #1: Putative multiheme cytochrome c

MacromoleculeName: Putative multiheme cytochrome c / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Desulfuromonas soudanensis (bacteria)
Molecular weightTheoretical: 21.697295 KDa
SequenceString: MKKVLVLAAA LVLAAAPAMA VIKDTKHDLS SGNVNGSGSN TDETCVFCHT PHGASASGTA PLWNRTNDTT PTGTYGNPTG TMNAVPLAA DVALTDAVLC LSCHDGSIGN TLTNPPNSLG ATALAVTATL SAGANLGADM SNDHPIGMSY GDAITGGDTE L VAAAGGLP ...String:
MKKVLVLAAA LVLAAAPAMA VIKDTKHDLS SGNVNGSGSN TDETCVFCHT PHGASASGTA PLWNRTNDTT PTGTYGNPTG TMNAVPLAA DVALTDAVLC LSCHDGSIGN TLTNPPNSLG ATALAVTATL SAGANLGADM SNDHPIGMSY GDAITGGDTE L VAAAGGLP LFSQTLSVAG AKTDVVWCSS CHDVHGKVGV STFLQVTNAA SALCTTCHSK

UniProtKB: Putative multiheme cytochrome c

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Macromolecule #2: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 2 / Number of copies: 64 / Formula: HEC
Molecular weightTheoretical: 620.519 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 32 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 10.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 2.0 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: 30.75 Å
Applied symmetry - Helical parameters - Δ&Phi: 51.44 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1241521
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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