7TFS | pdb_00007tfs

Cryo-EM of the OmcE nanowires from Geobacter sulfurreducens

• PDB DOI: https://doi.org/10.2210/pdb7TFS/pdb
• EM Map EMD-25879: EMDB EMDataResource

• Classification: ELECTRON TRANSPORT, PROTEIN FIBRIL
• Organism(s): Geobacter sulfurreducens
• Mutation(s): No 


• Deposited: 2022-01-07 Released: 2022-05-04 
• Deposition Author(s): Wang, F., Mustafa, K., Chan, C.H., Joshi, K., Hochbaum, A.I., Bond, D.R., Egelman, E.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing.

Wang, F., Mustafa, K., Suciu, V., Joshi, K., Chan, C.H., Choi, S., Su, Z., Si, D., Hochbaum, A.I., Egelman, E.H., Bond, D.R.

(2022) Nat Microbiol 7: 1291-1300

• PubMed: 35798889 
• DOI: https://doi.org/10.1038/s41564-022-01159-z
• Primary Citation Related Structures: 
  7TFS, 7TGG


• PubMed 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 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
Department of Chemistry, University of California, Irvine, Irvine, CA, USA.
Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA, USA.
Department of Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA.
Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Department of Chemistry, University of California, Irvine, Irvine, CA, USA. [e-mail].
Department of Materials Science and Engineering, Department of Molecular Biology and Biochemistry and Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA. [e-mail].
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA. [e-mail].
Department of Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 26.31 kDa 
• Atom Count: 1,626 
• Modeled Residue Count: 202 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	A	232	Geobacter sulfurreducens	Mutation(s): 0
UniProt
Find proteins for Q74FJ0 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74FJ0  Go to UniProtKB:  Q74FJ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Wang, F., Mustafa, K., Chan, C.H., Joshi, K., Hochbaum, A.I., Bond, D.R., Egelman, E.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM122510
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	K99GM138756

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references
• Version 1.2: 2024-12-25
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.3: 2025-05-14
  Changes: Data collection