1M19

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 

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

  • DOI: 10.1016/s0022-2836(02)01407-9
  • Structures With Same Primary Citation

  • 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 H3.2A, E135Xenopus laevisMutation(s): 0 
Gene Names: h3-5h3f3c
Find proteins for P02302 (Xenopus laevis)
Explore P02302 
Go to UniProtKB:  P02302
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4B, F102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.1C, G129Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
Go to UniProtKB:  P06897
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B.1D, H125Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Palindromic 146 Base Pair DNA FragmentI, J146N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMT
Query on IMT

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

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

Download CCD File 
I, J
GAMMA-AMINO-BUTANOIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
 Ligand Interaction
DIB
Query on DIB

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

Download CCD File 
I, J
BETA-ALANINE
C3 H7 N O2
UCMIRNVEIXFBKS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
E, I, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.045α = 90
b = 109.662β = 90
c = 183.018γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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