Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2BCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 201.63 kDa 
• Atom Count: 12237 
• Residue Count: 1066 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

3LJA

Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome

• DOI: 10.2210/pdb3LJA/pdb
• NDB: NA0439

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


• Deposited: 2010-01-26 Released: 2010-04-14 
• Deposition Author(s): Wu, B., Davey, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.259 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome

Wu, B., Davey, C.A.

(2010) J Mol Biol 398: 633-640

• PubMed: 20350553 
• DOI: 10.1016/j.jmb.2010.03.038
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Divalent metals associate with DNA in a site-selective manner, which can influence nucleosome positioning, mobility, compaction, and recognition by nuclear factors. We previously characterized divalent metal binding in the nucleosome core using hard (short-wavelength) X-rays allowing high-resolution crystallographic determination of the strongest affinity sites, which revealed that Mn(2+) associates with the DNA major groove in a sequence- and conformation-dependent manner. In this study, we obtained diffraction data with soft X-rays at the Mn(2+) absorption edge for a core particle crystal in the presence of 10 mM MnSO(4), mimicking prevailing Mg(2+) concentration in the nucleus. This provides an exceptional view of counterion binding in the nucleosome through identification of 45 divalent metal binding sites. In addition to that at the well-characterized major interparticle interface, only one other histone-divalent metal binding site is found, which corresponds to a symmetry-related counterpart on the 'free' H2B alpha1 helix C-terminus. This emphasizes the importance of the alpha-helix dipole in ion binding and suggests that the H2B motif may serve as a nucleation site in nucleosome compaction. The 43 sites associated with the DNA are characterized by (1) high-affinity direct coordination at the most electrostatically favorable major groove locations, (2) metal hydrate binding to the major groove, (3) direct coordination to phosphate groups at sites of high charge density, (4) metal hydrate binding in the minor groove, or (5) metal hydrate-divalent anion pairing. Metal hydrates are found within the minor groove only at locations displaying a narrow range of high-intermediate width and to which histone N-terminal tails are not associated or proximal. This indicates that divalent metals and histone tails can both collaborate and compete in minor groove association, which sheds light on nucleosome solubility and chromatin compaction behavior.

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Organizational Affiliation: 

Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.2	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	C, G	129	Xenopus laevis	Mutation(s): 0  Gene Names: LOC494591
Find proteins for P06897 (Xenopus laevis) Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B 1.1	D, H	122	Xenopus laevis	Mutation(s): 0
Find proteins for P02281 (Xenopus laevis) Go to UniProtKB:  P02281

Entity ID: 5
Molecule	Chains	Length	Organism
147mer DNA	I	147	N/A

Entity ID: 6
Molecule	Chains	Length	Organism
147mer DNA	J	147	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D, G, H	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	E, H, I, J	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.259 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.348	α = 90
b = 109.785	β = 90
c = 182.424	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-26 
• Released Date: 2010-04-14 
Deposition Author(s): Wu, B., Davey, C.A.

Revision History 

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-12
  Changes: Database references