6NEF

Outer Membrane Cytochrome S Filament from Geobacter Sulfurreducens

• PDB DOI: https://doi.org/10.2210/pdb6NEF/pdb
• EM Map EMD-9357: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Geobacter sulfurreducens PCA
• Mutation(s): No 


• Deposited: 2018-12-17 Released: 2019-07-03 
• Deposition Author(s): Filman, D.J., Marino, S.F., Ward, J.E., Yang, L., Mester, Z., Bullitt, E., Lovley, D.R., Strauss, M.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

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

Literature

Cryo-EM reveals the structural basis of long-range electron transport in a cytochrome-based bacterial nanowire.

Filman, D.J., Marino, S.F., Ward, J.E., Yang, L., Mester, Z., Bullitt, E., Lovley, D.R., Strauss, M.

(2019) Commun Biol 2: 219-219

• PubMed: 31240257 
• DOI: https://doi.org/10.1038/s42003-019-0448-9
• Primary Citation of Related Structures:  
  6NEF


• PubMed Abstract: 
  

  Electrically conductive pili from Geobacter species, termed bacterial nanowires, are intensely studied for their biological significance and potential in the development of new materials. Using cryo-electron microscopy, we have characterized nanowires from conductive G. sulfurreducens pili preparations that are composed solely of head-to-tail stacked monomers of the six-heme C-type cytochrome OmcS. The unique fold of OmcS - closely wrapped around a continuous stack of hemes that can serve as an uninterrupted path for electron transport - generates a scaffold that supports the unbranched chain of hemes along the central axis of the filament. We present here, at 3.4 Å resolution, the structure of this cytochrome-based filament and discuss its possible role in long-range biological electron transport.

---

Organizational Affiliation: 

1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115 USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 9-mer - A9 

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

Macromolecule Content

• Total Structure Weight: 46.72 kDa 
• Atom Count: 3,273 
• Modelled Residue Count: 407 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type cytochrome OmcS	A	407	Geobacter sulfurreducens PCA	Mutation(s): 0
UniProt
Find proteins for Q74A86 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74A86  Go to UniProtKB:  Q74A86

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
MG	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0238
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Filman, D.J., Marino, S.F., Ward, J.E., Yang, L., Mester, Z., Bullitt, E., Lovley, D.R., Strauss, M.

---

Funding Organization	Location	Grant Number
Other government	United States	N00014-16-1-2526

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 2.0: 2019-09-11
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary