2Q2K | pdb_00002q2k

Structure of nucleic-acid binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.297 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2Q2K

This is version 1.2 of the entry. See complete history

Literature

Segrosome structure revealed by a complex of ParR with centromere DNA.

Schumacher, M.A.Glover, T.C.Brzoska, A.J.Jensen, S.O.Dunham, T.D.Skurray, R.A.Firth, N.

(2007) Nature 450: 1268-1271

  • DOI: https://doi.org/10.1038/nature06392
  • Primary Citation Related Structures: 
    2Q2K

  • PubMed Abstract: 

    The stable inheritance of genetic material depends on accurate DNA partition. Plasmids serve as tractable model systems to study DNA segregation because they require only a DNA centromere, a centromere-binding protein and a force-generating ATPase. The centromeres of partition (par) systems typically consist of a tandem arrangement of direct repeats. The best-characterized par system contains a centromere-binding protein called ParR and an ATPase called ParM. In the first step of segregation, multiple ParR proteins interact with the centromere repeats to form a large nucleoprotein complex of unknown structure called the segrosome, which binds ParM filaments. pSK41 ParR binds a centromere consisting of multiple 20-base-pair (bp) tandem repeats to mediate both transcription autoregulation and segregation. Here we report the structure of the pSK41 segrosome revealed in the crystal structure of a ParR-DNA complex. In the crystals, the 20-mer tandem repeats stack pseudo-continuously to generate the full-length centromere with the ribbon-helix-helix (RHH) fold of ParR binding successive DNA repeats as dimer-of-dimers. Remarkably, the dimer-of-dimers assemble in a continuous protein super-helical array, wrapping the DNA about its positive convex surface to form a large segrosome with an open, solenoid-shaped structure, suggesting a mechanism for ParM capture and subsequent plasmid segregation.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of Texas, M.D. Anderson Cancer Center, Unit 1000, Houston, TX 77030, USA. maschuma@mdanderson.org

Macromolecule Content 

  • Total Structure Weight: 22.93 kDa 
  • Atom Count: 1,184 
  • Modeled Residue Count: 109 
  • Deposited Residue Count: 160 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical proteinB [auth A],
C [auth B]
70Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for O87365 (Staphylococcus aureus)
Explore O87365 
Go to UniProtKB:  O87365
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87365
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*TP*AP*TP*AP*(5IU)P*AP*CP*(5IU)P*AP*GP*TP*AP*TP*AP*TP*AP*CP*T)-3')A [auth F]20N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
D [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.297 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.3α = 90
b = 56.3β = 90
c = 232.5γ = 120
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations