3PMQ

Crystal structure of the outer membrane decaheme cytochrome MtrF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.306 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of a bacterial cell surface decaheme electron conduit.

Clarke, T.A.Edwards, M.J.Gates, A.J.Hall, A.White, G.F.Bradley, J.Reardon, C.L.Shi, L.Beliaev, A.S.Marshall, M.J.Wang, Z.Watmough, N.J.Fredrickson, J.K.Zachara, J.M.Butt, J.N.Richardson, D.J.

(2011) Proc Natl Acad Sci U S A 108: 9384-9389

  • DOI: https://doi.org/10.1073/pnas.1017200108
  • Primary Citation of Related Structures:  
    3PMQ

  • PubMed Abstract: 

    Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along "nanowire" appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split β-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.


  • Organizational Affiliation

    Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Decaheme cytochrome c MtrF669Shewanella oneidensis MR-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8EG32 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EG32 
Go to UniProtKB:  Q8EG32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EG32
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 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
L [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.306 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 256.64α = 90
b = 256.64β = 90
c = 256.64γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHELXSphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-05-31
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary