structure of no-dna complex

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid.

Tonthat, N.K.Milam, S.L.Chinnam, N.Whitfill, T.Margolin, W.Schumacher, M.A.

(2013) Proc Natl Acad Sci U S A 110: 10586-10591

  • DOI: https://doi.org/10.1073/pnas.1221036110
  • Primary Citation of Related Structures:  
    4GCK, 4GCL, 4GCT, 4GFK, 4GFL

  • PubMed Abstract: 

    The spatial and temporal control of Filamenting temperature sensitive mutant Z (FtsZ) Z-ring formation is crucial for proper cell division in bacteria. In Escherichia coli, the synthetic lethal with a defective Min system (SlmA) protein helps mediate nucleoid occlusion, which prevents chromosome fragmentation by binding FtsZ and inhibiting Z-ring formation over the nucleoid. However, to perform its function, SlmA must be bound to the nucleoid. To deduce the basis for this chromosomal requirement, we performed biochemical, cellular, and structural studies. Strikingly, structures show that SlmA dramatically distorts DNA, allowing it to bind as an orientated dimer-of-dimers. Biochemical data indicate that SlmA dimer-of-dimers can spread along the DNA. Combined structural and biochemical data suggest that this DNA-activated SlmA oligomerization would prevent FtsZ protofilament propagation and bundling. Bioinformatic analyses localize SlmA DNA sites near membrane-tethered chromosomal regions, and cellular studies show that SlmA inhibits FtsZ reservoirs from forming membrane-tethered Z rings. Thus, our combined data indicate that SlmA DNA helps block Z-ring formation over chromosomal DNA by forming higher-order protein-nucleic acid complexes that disable FtsZ filaments from coalescing into proper structures needed for Z-ring creation.

  • Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoid occlusion factor SlmA
A, B, C, D
212Klebsiella pneumoniae 342Mutation(s): 0 
Gene Names: slmAKPK_0113
Find proteins for B5XTG2 (Klebsiella pneumoniae (strain 342))
Explore B5XTG2 
Go to UniProtKB:  B5XTG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5XTG2
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')E [auth W],
F [auth Z]
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.49α = 90
b = 80.75β = 90
c = 201.3γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references