3VEA

Crystal Structure of matP-matS23mer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for a protein-mediated DNA-bridging mechanism that functions in condensation of the E. coli chromosome.

Dupaigne, P.Tonthat, N.K.Espeli, O.Whitfill, T.Boccard, F.Schumacher, M.A.

(2012) Mol Cell 48: 560-571

  • DOI: https://doi.org/10.1016/j.molcel.2012.09.009
  • Primary Citation of Related Structures:  
    3VEA, 3VEB, 4D8J

  • PubMed Abstract: 

    The E. coli chromosome is condensed into insulated regions termed macrodomains (MDs), which are essential for genomic packaging. How chromosomal MDs are specifically organized and compacted is unknown. Here, we report studies revealing the molecular basis for Terminus-containing (Ter) chromosome condensation by the Ter-specific factor MatP. MatP contains a tripartite fold with a four-helix bundle DNA-binding motif, ribbon-helix-helix and C-terminal coiled-coil. Strikingly, MatP-matS structures show that the MatP coiled-coils form bridged tetramers that flexibly link distant matS sites. Atomic force microscopy and electron microscopy studies demonstrate that MatP alone loops DNA. Mutation of key coiled-coil residues destroys looping and causes a loss of Ter condensation in vivo. Thus, these data reveal the molecular basis for a protein-mediated DNA-bridging mechanism that mediates condensation of a large chromosomal domain in enterobacteria.


  • Organizational Affiliation

    Centre de Génétique Moléculaire du CNRS, Associé à l'Université Paris-Sud, 91198 Gif-sur-Yvette, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrodomain Ter proteinA [auth B],
D [auth A]
151Yersinia pestisMutation(s): 0 
Gene Names: matPy2737YPO1433YP_0877
UniProt
Find proteins for Q8ZG78 (Yersinia pestis)
Explore Q8ZG78 
Go to UniProtKB:  Q8ZG78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZG78
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'B [auth N]23N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'C [auth M]23N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.98α = 90
b = 111.31β = 90
c = 169.14γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description