1KX5

X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution

Davey, C.A.Sargent, D.F.Luger, K.Maeder, A.W.Richmond, T.J.

(2002) J.Mol.Biol. 319: 1097-1113

  • DOI: 10.1016/S0022-2836(02)00386-8
  • Primary Citation of Related Structures:  
  • Also Cited By: 3B6G, 3B6F

  • PubMed Abstract: 
  • Solvent binding in the nucleosome core particle containing a 147 base pair, defined-sequence DNA is characterized from the X-ray crystal structure at 1.9 A resolution. A single-base-pair increase in DNA length over that used previously results in sub ...

    Solvent binding in the nucleosome core particle containing a 147 base pair, defined-sequence DNA is characterized from the X-ray crystal structure at 1.9 A resolution. A single-base-pair increase in DNA length over that used previously results in substantially improved clarity of the electron density and accuracy for the histone protein and DNA atomic coordinates. The reduced disorder has allowed for the first time extensive modeling of water molecules and ions. Over 3000 water molecules and 18 ions have been identified. Water molecules acting as hydrogen-bond bridges between protein and DNA are approximately equal in number to the direct hydrogen bonds between these components. Bridging water molecules have a dual role in promoting histone-DNA association not only by providing further stability to direct protein-DNA interactions, but also by enabling formation of many additional interactions between more distantly related elements. Water molecules residing in the minor groove play an important role in facilitating insertion of arginine side-chains. Water structure at the interface of the histones and DNA provides a means of accommodating intrinsic DNA conformational variation, thus limiting the sequence dependency of nucleosome positioning while enhancing mobility. Monovalent anions are bound near the N termini of histone alpha-helices that are not occluded by DNA phosphate groups. Their location in proximity to the DNA phosphodiester backbone suggests that they damp the electrostatic interaction between the histone proteins and the DNA. Divalent cations are bound at specific sites in the nucleosome core particle and contribute to histone-histone and histone-DNA interparticle interactions. These interactions may be relevant to nucleosome association in arrays.


    Related Citations: 
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
      Luger, K.,Maeder, A.W.,Richmond, R.K.,Sargent, D.F.,Richmond, T.J.
      (1997) Nature 389: 251
    • DNA-dependent divalent cation binding in the nucleosome core particle.
      Davey, C.A.,Richmond, T.J.
      (2002) Proc.Natl.Acad.Sci.USA 99: 11169
    • DNA structure in the nucleosome core
      Richmond, T.J.,Davey, C.A.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Institut für Molekularbiologie und Biophysik, ETH-Hönggerberg, CH-8093 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
histone H3
A, E
135Xenopus laevisMutation(s): 0 
N/A
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
histone H4
B, F
102Xenopus laevisMutation(s): 0 
N/A
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
histone H2A.1
C, G
128Xenopus laevisMutation(s): 0 
N/A
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
histone H2B.2
D, H
125Xenopus laevisMutation(s): 0 
N/A
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'(ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT)3')I147Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'(ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT)3')J147Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.950α = 90.00
b = 181.170β = 90.00
c = 109.490γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance