1M1A

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands

Suto, R.K.Edayathumangalam, R.S.White, C.L.Melander, C.Gottesfeld, J.M.Dervan, P.B.Luger, K.

(2003) J.MOL.BIOL. 326: 371-380

  • Primary Citation of Related Structures:  1M18, 1M19

  • PubMed Abstract: 
  • We determined the crystal structures of three nucleosome core particles in complex with site-specific DNA-binding ligands, the pyrrole-imidazole polyamides. While the structure of the histone octamer and its interaction with the DNA remain unaffected ...

    We determined the crystal structures of three nucleosome core particles in complex with site-specific DNA-binding ligands, the pyrrole-imidazole polyamides. While the structure of the histone octamer and its interaction with the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes significant structural changes at the ligand-binding sites and in adjacent regions to accommodate the ligands. Our findings suggest that twist diffusion occurs over long distances through tightly bound nucleosomal DNA. This may be relevant to the mechanism of ATP-dependent and spontaneous nucleosome translocation, and to the effect of bound factors on nucleosome dynamics.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisGene Names: h3f3c
Find proteins for P02302 (Xenopus laevis)
Go to UniProtKB:  P02302
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisN/A
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.1
C, G
129Xenopus laevisN/A
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B.1
D, H
125Xenopus laevisN/A
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 1
MoleculeChainsLengthOrganism
Palindromic 146 Base Pair DNA FragmentI,J146N/A
Small Molecules
Ligands 6 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
BAL
Query on BAL

Download SDF File 
Download CCD File 
J
BETA-ALANINE
C3 H7 N O2
UCMIRNVEIXFBKS-UHFFFAOYSA-N
 Ligand Interaction
IMT
Query on IMT

Download SDF File 
Download CCD File 
J
4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID
C5 H7 N3 O2
PPQDQYBXCYQCNH-UHFFFAOYSA-N
 Ligand Interaction
DIB
Query on DIB

Download SDF File 
Download CCD File 
J
3-AMINO-(DIMETHYLPROPYLAMINE)
C5 H14 N2
IUNMPGNGSSIWFP-UHFFFAOYSA-N
 Ligand Interaction
PYB
Query on PYB

Download SDF File 
Download CCD File 
J
4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID
C6 H8 N2 O2
MUEOQEUSJMFYHV-UHFFFAOYSA-N
 Ligand Interaction
ABU
Query on ABU

Download SDF File 
Download CCD File 
J
GAMMA-AMINO-BUTANOIC ACID
GAMMA(AMINO)-BUTYRIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.719α = 90.00
b = 109.196β = 90.00
c = 177.353γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance