3VEA | pdb_00003vea

Crystal Structure of matP-matS23mer

• PDB DOI: https://doi.org/10.2210/pdb3VEA/pdb
• NAKB: 3VEA

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-07 Released: 2012-11-21 
• Deposition Author(s): Schumacher, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.250 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

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

• PubMed: 23084832 
• DOI: https://doi.org/10.1016/j.molcel.2012.09.009
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 50.06 kDa 
• Atom Count: 3,487 
• Modeled Residue Count: 344 
• Deposited Residue Count: 348 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrodomain Ter protein	A [auth B], D [auth A]	151	Yersinia pestis	Mutation(s): 0  Gene Names: matP, y2737, YPO1433, YP_0877
UniProt
Find proteins for Q8ZG78 (Yersinia pestis) Explore Q8ZG78  Go to UniProtKB:  Q8ZG78

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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]	23	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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]	23	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.250 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.98	α = 90
b = 111.31	β = 90
c = 169.14	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Schumacher, M.A.

Revision History  

• 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