3MGR

Binding of Rubidium ions to the Nucleosome Core Particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Perturbations in nucleosome structure from heavy metal association.

Mohideen, K.Muhammad, R.Davey, C.A.

(2010) Nucleic Acids Res 38: 6301-6311

  • DOI: 10.1093/nar/gkq420
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Heavy metals have the potential to engage in strong bonding interactions and can thus function in essential as well as toxic or therapeutic capacities. We conducted crystallographic analyses of heavy cation binding to the nucleosome core particle and ...

    Heavy metals have the potential to engage in strong bonding interactions and can thus function in essential as well as toxic or therapeutic capacities. We conducted crystallographic analyses of heavy cation binding to the nucleosome core particle and found that Co(2+) and Ni(2+) preferentially associate with the DNA major groove, in a sequence- and conformation-dependent manner. Conversely, Rb(+) and Cs(+) are found to bind only opportunistically to minor groove elements of the DNA, in particular at narrow AT dinucleotide sites. Furthermore, relative to Mn(2+) the aggressive coordination of Co(2+) and Ni(2+) to guanine bases is observed to induce a shift in histone-DNA register around the nucleosome center by stabilizing DNA stretching over one region accompanied by expulsion of two bases at an opposing location. These 'softer' transition metals also associate with multiple histone protein sites, including inter-nucleosomal cross-linking, and display a proclivity for coordination to histidine. Sustained binding and the ability to induce structural perturbations at specific locations in the nucleosome may contribute to genetic and epigenetic mechanisms of carcinogenesis mediated by Co(2+) and Ni(2+).


    Organizational Affiliation

    Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
Gene Names: Histone 3 or H3
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Gene Names: Histone 4 or H4
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
119Xenopus laevisMutation(s): 0 
Gene Names: Histone 2A or H2ALOC494591h2ac14hist1h2ajXELAEV_18003602mg
Find proteins for Q6AZJ8 (Xenopus laevis)
Go to UniProtKB:  Q6AZJ8

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
125Xenopus laevisMutation(s): 0 
Gene Names: Histone 2B or H2B
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsLengthOrganism
DNA (147-MER)I147N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
DNA (147-MER)J147N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RB
Query on RB

Download CCD File 
D, H, I, J
RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
E, I, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, D, E, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.462α = 90
b = 109.681β = 90
c = 182.213γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-05-21
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description