Biological Assembly 1  

 3D View: Structure

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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: 198980.75 
• Atom Count: 11953 
• Residue Count: 1274 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

1P3M

Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants

• DOI: 10.2210/pdb1P3M/pdb
• NDB: PD0421

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


• Deposited: 2003-04-17 Released: 2004-02-24 
• Deposition Author(s): Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.270 
• R-Value Work: 0.209 

Literature

Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions

Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K.

(2004) EMBO J. 23: 260-271

• PubMed: 14739929 
• DOI: 10.1038/sj.emboj.7600046
• Primary Citation of Related Structures:  
  1P3P, 1P3O, 1P3L, 1P3K, 1P3I, 1P3G, 1P3F, 1P3B, 1P3A, 1P34


• PubMed Abstract: 
  

Here we describe 11 crystal structures of nucleosome core particles containing individual point mutations in the structured regions of histones H3 and H4. The mutated residues are located at the two protein-DNA interfaces flanking the nucleosomal dyad. Five of the mutations partially restore the in vivo effects of SWI/SNF inactivation in yeast. We find that even nonconservative mutations of these residues (which exhibit a distinct phenotype in vivo) have only moderate effects on global nucleosome structure. Rather, local protein-DNA interactions are disrupted and weakened in a subtle and complex manner. The number of lost protein-DNA interactions correlates directly with an increased propensity of the histone octamer to reposition with respect to the DNA, and with an overall destabilization of the nucleosome. Thus, the disruption of only two to six of the approximately 120 direct histone-DNA interactions within the nucleosome has a pronounced effect on nucleosome mobility and stability. This has implications for our understanding of how these structures are made accessible to the transcription and replication machinery in vivo.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H3	A, E	135	Xenopus laevis	Mutation(s): 0
Find proteins for P84233 (Xenopus laevis) Go to UniProtKB:  P84233

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	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	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 146bp Human Alpha-Satellite DNA fragment	I,J	146	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.270 
• R-Value Work: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 105.766	α = 90.00
b = 109.634	β = 90.00
c = 181.508	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-17 
• Released Date: 2004-02-24 
• Deposition Author(s): Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K.

Revision History 

• Version 1.0: 2004-02-24
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance