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 2.0 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: https://doi.org/10.1016/s0022-2836(02)01407-9
  • Primary Citation of Related Structures:  
    1M18, 1M19, 1M1A

  • 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 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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3CC [auth A],
G [auth E]
135Xenopus laevisMutation(s): 0 
Gene Names: h3-5
UniProt
Find proteins for P02302 (Xenopus laevis)
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Go to UniProtKB:  P02302
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UniProt GroupP02302
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]
102Xenopus laevisMutation(s): 0 
Gene Names: LOC121398084
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1E [auth C],
I [auth G]
129Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2BF [auth D],
J [auth H]
125Xenopus laevisMutation(s): 0 
Gene Names: LOC108704303
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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UniProt GroupP02281
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Entity ID: 1
MoleculeChains LengthOrganismImage
Palindromic 146 Base Pair DNA FragmentA [auth I],
B [auth J]
146synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMT
Query on IMT

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BA [auth I],
BB [auth J],
MB [auth J],
Q [auth I],
QA [auth J]
4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID
C5 H7 N3 O2
PPQDQYBXCYQCNH-UHFFFAOYSA-N
PYB
Query on PYB

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CA [auth I]
CB [auth J]
DA [auth I]
DB [auth J]
EA [auth I]
CA [auth I],
CB [auth J],
DA [auth I],
DB [auth J],
EA [auth I],
EB [auth J],
GA [auth I],
GB [auth J],
HA [auth I],
HB [auth J],
IA [auth I],
IB [auth J],
JA [auth I],
JB [auth J],
NB [auth J],
OB [auth J],
PB [auth J],
R [auth I],
RA [auth J],
RB [auth J],
S [auth I],
SA [auth J],
SB [auth J],
T [auth I],
TA [auth J],
TB [auth J],
UB [auth J],
V [auth I],
VA [auth J],
W [auth I],
WA [auth J],
X [auth I],
XA [auth J],
Y [auth I],
YA [auth J]
4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID
C6 H8 N2 O2
MUEOQEUSJMFYHV-UHFFFAOYSA-N
ABU
Query on ABU

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FA [auth I],
FB [auth J],
QB [auth J],
U [auth I],
UA [auth J]
GAMMA-AMINO-BUTANOIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
DIB
Query on DIB

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AA [auth I],
AB [auth J],
LA [auth I],
LB [auth J],
WB [auth J]
3-AMINO-(DIMETHYLPROPYLAMINE)
C5 H14 N2
IUNMPGNGSSIWFP-UHFFFAOYSA-N
BAL
Query on BAL

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KA [auth I],
KB [auth J],
VB [auth J],
Z [auth I],
ZA [auth J]
BETA-ALANINE
C3 H7 N O2
UCMIRNVEIXFBKS-UHFFFAOYSA-N
MN
Query on MN

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K [auth I]
L [auth I]
M [auth I]
MA [auth J]
N [auth I]
K [auth I],
L [auth I],
M [auth I],
MA [auth J],
N [auth I],
NA [auth J],
O [auth I],
OA [auth J],
P [auth I],
PA [auth J],
XB [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
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  (Full details and data files)

  • 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
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary