9YUQ | pdb_00009yuq

A Bundled Antiparallel Cytochrome Nanowire Produced by Desulfuromonas soudanensis WTL


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 9YUQ

This is version 1.1 of the entry. See complete history

Literature

A bundled anti-parallel cytochrome nanowire structure suggests roles in cell-cell electron transfer and biofilm formation.

Petersen, H.A.Chan, C.H.Carpenter, G.O.Tabari, M.Z.Fields, J.L.Zia, A.Rich-New, S.T.Hochbaum, A.I.Bond, D.R.Wang, F.

(2026) mBio : e0090626-e0090626

  • DOI: https://doi.org/10.1128/mbio.00906-26
  • Primary Citation Related Structures: 
    9YUQ

  • PubMed 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. This process is primarily studied in Geobacter sulfurreducens , 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 Desulfuromonas soudanensis 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 in vivo confirmation within intact biofilms remains a future goal. Furthermore, a similar cytochrome bundle structure was observed in Geobacter metallireducens , 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. IMPORTANCE 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.

Macromolecule Content 

  • Total Structure Weight: 388.15 kDa 
  • Atom Count: 24,832 
  • Modeled Residue Count: 3,168 
  • Deposited Residue Count: 3,488 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative multiheme cytochrome c218Desulfuromonas soudanensisMutation(s): 0 
UniProt
Find proteins for A0A0M4DKA8 (Desulfuromonas soudanensis)
Explore A0A0M4DKA8 
Go to UniProtKB:  A0A0M4DKA8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4DKA8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC

Query on HEC



Download:Ideal Coordinates CCD File
AB [auth C]
AC [auth G]
BA [auth M]
BB [auth C]
BC [auth G]
AB [auth C],
AC [auth G],
BA [auth M],
BB [auth C],
BC [auth G],
BD [auth S],
CA [auth M],
CB [auth C],
CD [auth S],
DA [auth L],
DD [auth S],
EA [auth L],
EC [auth P],
ED [auth T],
FB [auth C],
FC [auth P],
FD [auth T],
GB [auth C],
GC [auth P],
HA [auth L],
HB [auth C],
IA [auth L],
IB [auth D],
JA [auth K],
JC [auth P],
KA [auth K],
KC [auth P],
LB [auth D],
LC [auth P],
MB [auth D],
MC [auth Q],
NA [auth K],
NB [auth E],
OA [auth K],
OB [auth E],
PA [auth J],
PC [auth Q],
Q [auth N],
QA [auth J],
QC [auth Q],
R [auth N],
RB [auth E],
RC [auth R],
S [auth N],
SB [auth E],
SC [auth R],
TA [auth J],
TB [auth F],
UA [auth J],
UB [auth F],
V [auth N],
VA [auth I],
VC [auth R],
W [auth N],
WA [auth I],
WC [auth R],
X [auth M],
XA [auth I],
XB [auth F],
XC [auth S],
Y [auth M],
YB [auth F],
YC [auth S],
ZB [auth G]
HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth M]
AD [auth S]
CC [auth G]
DB [auth C]
DC [auth G]
AA [auth M],
AD [auth S],
CC [auth G],
DB [auth C],
DC [auth G],
EB [auth C],
FA [auth L],
GA [auth L],
GD [auth T],
HC [auth P],
HD [auth T],
IC [auth P],
JB [auth D],
KB [auth D],
LA [auth K],
MA [auth K],
NC [auth Q],
OC [auth Q],
PB [auth E],
QB [auth E],
RA [auth J],
SA [auth J],
T [auth N],
TC [auth R],
U [auth N],
UC [auth R],
VB [auth F],
WB [auth F],
YA [auth I],
Z [auth M],
ZA [auth I],
ZC [auth S]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesSC0024303

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references