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- PDB-9yuq: A Bundled Antiparallel Cytochrome Nanowire Produced by Desulfurom... -

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Basic information

Entry
Database: PDB / ID: 9yuq
TitleA Bundled Antiparallel Cytochrome Nanowire Produced by Desulfuromonas soudanensis WTL
ComponentsPutative multiheme cytochrome c
KeywordsELECTRON TRANSPORT / multi-heme cytochrome / nanowire / EET / cryo-EM
Function / homologyDoubled CXXCH motif / Doubled CXXCH motif (Paired_CXXCH_1) / Multiheme cytochrome superfamily / HEME C / Putative multiheme cytochrome c
Function and homology information
Biological speciesDesulfuromonas soudanensis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsPetersen, H.A. / Chan, C.H. / Bond, D.R. / Wang, F.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.1Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Putative multiheme cytochrome c
M: Putative multiheme cytochrome c
L: Putative multiheme cytochrome c
K: Putative multiheme cytochrome c
J: Putative multiheme cytochrome c
I: Putative multiheme cytochrome c
C: Putative multiheme cytochrome c
D: Putative multiheme cytochrome c
E: Putative multiheme cytochrome c
F: Putative multiheme cytochrome c
G: Putative multiheme cytochrome c
P: Putative multiheme cytochrome c
Q: Putative multiheme cytochrome c
R: Putative multiheme cytochrome c
S: Putative multiheme cytochrome c
T: Putative multiheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,152112
Polymers347,15716
Non-polymers40,99696
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative multiheme cytochrome c


Mass: 21697.295 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Desulfuromonas soudanensis (bacteria) / References: UniProt: A0A0M4DKA8
#2: Chemical...
ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Multi-heme cytochrome nanowire / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Desulfuromonas soudanensis (bacteria) / Strain: WTL
Buffer solutionpH: 10.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 51.44 ° / Axial rise/subunit: 30.75 Å / Axial symmetry: C1
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1241521 / Symmetry type: HELICAL
RefinementHighest resolution: 3.11 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00625392
ELECTRON MICROSCOPYf_angle_d1.39936048
ELECTRON MICROSCOPYf_dihedral_angle_d17.9783774
ELECTRON MICROSCOPYf_chiral_restr0.0463808
ELECTRON MICROSCOPYf_plane_restr0.0054432

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