Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 8-mer -A8 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 206583.70 
• Atom Count: 12501 
• Residue Count: 1274 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

1M19

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

• DOI: 10.2210/pdb1M19/pdb
• NDB: PD0329

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli


• Deposited: 2002-06-18 Released: 2003-02-18 
• Deposition Author(s): Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.253 
• R-Value Work: 0.214 

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

• PubMed: 12559907 
• Primary Citation of Related Structures:  
  1M1A, 1M18


• 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.2	A, E	135	Xenopus laevis	Mutation(s): 0  Gene Names: h3f3c
Find proteins for P02302 (Xenopus laevis) Go to UniProtKB:  P02302

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	102	Xenopus laevis	Mutation(s): 0
Find proteins for P62799 (Xenopus laevis) Go to UniProtKB:  P62799

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A.1	C, G	129	Xenopus laevis	Mutation(s): 0
Find proteins for P06897 (Xenopus laevis) Go to UniProtKB:  P06897

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B.1	D, H	125	Xenopus laevis	Mutation(s): 0
Find proteins for P02281 (Xenopus laevis) Go to UniProtKB:  P02281

Entity ID: 1
Molecule	Chains	Length	Organism
Palindromic 146 Base Pair DNA Fragment	I,J	146	N/A

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	E, I, J	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
BAL	I, J	BETA-ALANINE C3 H7 N O2 UCMIRNVEIXFBKS-UHFFFAOYSA-N
IMT	I, J	4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID C5 H7 N3 O2 PPQDQYBXCYQCNH-UHFFFAOYSA-N
DIB	I, J	3-AMINO-(DIMETHYLPROPYLAMINE) C5 H14 N2 IUNMPGNGSSIWFP-UHFFFAOYSA-N
PYB	I, J	4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID C6 H8 N2 O2 MUEOQEUSJMFYHV-UHFFFAOYSA-N
ABU	I, J	GAMMA-AMINO-BUTANOIC ACID GAMMA(AMINO)-BUTYRIC ACID C4 H9 N O2 BTCSSZJGUNDROE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.253 
• R-Value Work: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 107.045	α = 90.00
b = 109.662	β = 90.00
c = 183.018	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-18 
• Released Date: 2003-02-18 
• Deposition Author(s): Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K.

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