1M1A | pdb_00001m1a

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

• PDB DOI: https://doi.org/10.2210/pdb1M1A/pdb
• NAKB: 1M1A

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): synthetic construct, Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.65 Å
• R-Value Free: 
  0.267 (Depositor) 
• R-Value Work: 
  0.223 (Depositor) 

Starting Model: experimental

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 Biology 326: 371-380

• PubMed: 12559907 
• DOI: https://doi.org/10.1016/s0022-2836(02)01407-9
• Primary Citation 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.

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 200.86 kDa 
• Atom Count: 12,378 
• Modeled Residue Count: 1,059 
• Deposited Residue Count: 1,274 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3C	C [auth A], G [auth E]	135	Xenopus laevis	Mutation(s): 0  Gene Names: h3-5
UniProt
Find proteins for P02302 (Xenopus laevis) Explore P02302  Go to UniProtKB:  P02302

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], H [auth F]	102	Xenopus laevis	Mutation(s): 0  Gene Names: LOC121398084
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	E [auth C], I [auth G]	129	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	F [auth D], J [auth H]	125	Xenopus laevis	Mutation(s): 0  Gene Names: LOC108704303
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Palindromic 146 Base Pair DNA Fragment	A [auth I], B [auth J]	146	synthetic construct

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMT	T [auth J], U [auth J]	4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID C5 H7 N3 O2 PPQDQYBXCYQCNH-UHFFFAOYSA-N
PYB	AA [auth J], BA [auth J], V [auth J], W [auth J], Y [auth J], Z [auth J]	4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID C6 H8 N2 O2 MUEOQEUSJMFYHV-UHFFFAOYSA-N
ABU	X [auth J]	GAMMA-AMINO-BUTANOIC ACID C4 H9 N O2 BTCSSZJGUNDROE-UHFFFAOYSA-N
DIB	DA [auth J]	3-AMINO-(DIMETHYLPROPYLAMINE) C5 H14 N2 IUNMPGNGSSIWFP-UHFFFAOYSA-N
BAL	CA [auth J]	BETA-ALANINE C3 H7 N O2 UCMIRNVEIXFBKS-UHFFFAOYSA-N
MN	EA [auth E], K [auth I], L [auth I], M [auth I], N [auth I], O [auth I], P [auth J], Q [auth J], R [auth J], S [auth J]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.719	α = 90
b = 109.196	β = 90
c = 177.353	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2024-02-14
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary