3VEB

Crystal Structure of Matp-matS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

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This is version 1.1 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Macrodomain Ter proteinD [auth A],
A [auth B]
151Yersinia pestisMutation(s): 0 
Gene Names: matPYPO1433y2737YP_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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*G)-3'B [auth N]16N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*AP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*G)-3'C [auth M]16N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth N],
F [auth N],
G [auth M]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.3α = 90
b = 102.3β = 90
c = 193.57γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
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