Biological Assembly 1  

 3D View: Structure | Electron Density

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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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 198996.84 
• Atom Count: 12041 
• Residue Count: 1274 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

3C1B

The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure

• DOI: 10.2210/pdb3C1B/pdb
• NDB: PD1077

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


• Deposited: 2008-01-22 Released: 2008-10-07 
• Deposition Author(s): Lu, X., Simon, M., Chodaparambil, J., Hansen, J., Shokat, K., Luger, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.270 
• R-Value Work: 0.240 

Literature

The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure.

Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M., Luger, K.

(2008) Nat.Struct.Mol.Biol. 15: 1122-1124

• PubMed: 18794842 
• DOI: 10.1038/nsmb.1489
• Primary Citation of Related Structures:  
  3C1C


• PubMed Abstract: 
  

Histone methylation regulates chromatin function dependent on the site and degree of the modification. In addition to creating binding sites for proteins, methylated lysine residues are likely to influence chromatin structure directly. Here we present crystal structures of nucleosomes reconstituted with methylated histones and investigate the folding behavior of resulting arrays. We demonstrate that dimethylation of histone H3 at lysine residue 79 locally alters the nucleosomal surface, whereas trimethylation of H4 at lysine residue 20 affects higher-order structure.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, 1385 Center Avenue, Fort Collins, Colorado 80523-1870, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3-like	A, E	135	Xenopus laevis	Mutation(s): 0
Find proteins for P84233 (Xenopus laevis) Go to UniProtKB:  P84233

Entity ID: 2
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: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1	C, G	129	Xenopus laevis	Mutation(s): 0
Find proteins for P06897 (Xenopus laevis) Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone 2, H2bf	D, H	125	Xenopus tropicalis	Mutation(s): 0  Gene Names: hist2h2bf (LOC108648866)
Find proteins for Q28D68 (Xenopus tropicalis) Go to UniProtKB:  Q28D68

Entity ID: 5
Molecule	Chains	Length	Organism
Palindromic 146bp Human Alpha satellite DNA	I,J	146	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ML3	B, F	L-peptide linking	C8 H19 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.270 
• R-Value Work: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 105.670	α = 90.00
b = 109.830	β = 90.00
c = 181.030	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-22 
• Released Date: 2008-10-07 
• Deposition Author(s): Lu, X., Simon, M., Chodaparambil, J., Hansen, J., Shokat, K., Luger, K.

Revision History 

• Version 1.0: 2008-10-07
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance