7LQ5

Cryo-EM structure of OmcZ nanowire from Geobacter sulfurreducens


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity.

Gu, Y.Guberman-Pfeffer, M.J.Srikanth, V.Shen, C.Giska, F.Gupta, K.Londer, Y.Samatey, F.A.Batista, V.S.Malvankar, N.S.

(2023) Nat Microbiol 8: 284-298

  • DOI: https://doi.org/10.1038/s41564-022-01315-5
  • Primary Citation of Related Structures:  
    7LQ5

  • PubMed Abstract: 

    OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm -1 ). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.


  • Organizational Affiliation

    Microbial Sciences Institute, Yale University, West Haven, CT, USA. ygu@mrc-lmb.cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c
A, B, C
258Geobacter sulfurreducens PCAMutation(s): 0 
UniProt
Find proteins for Q74BG5 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Explore Q74BG5 
Go to UniProtKB:  Q74BG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ74BG5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
AA [auth C]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
AA [auth C],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.08
MODEL REFINEMENTPHENIXdev_3689

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1749662

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references