5OMX

X-ray Structure of the H2A-N38C Nucleosome Core Particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability.

Frouws, T.D.Barth, P.D.Richmond, T.J.

(2018) J Mol Biol 430: 45-57

  • DOI: 10.1016/j.jmb.2017.10.029
  • Primary Citation of Related Structures:  
    5ONG, 5OMX, 5ONW

  • PubMed Abstract: 
  • We engineered nucleosome core particles (NCPs) with two site-specific cysteine crosslinks that increase the stability of the particle. The first disulfide was introduced between the two copies of H2A via an H2A-N38C point mutation, effectively crossl ...

    We engineered nucleosome core particles (NCPs) with two site-specific cysteine crosslinks that increase the stability of the particle. The first disulfide was introduced between the two copies of H2A via an H2A-N38C point mutation, effectively crosslinking the two H2A/H2B heterodimers together to stabilize the histone octamer against H2A/H2B dimer dissociation. The second crosslink was engineered between an R40C point mutation on the N-terminal tail of H3 and the NCP DNA ends by the introduction of a convertible nucleotide. This crosslink maintains the nucleosome DNA in a fixed translational setting relative to the histone octamer and prevents dilution-driven dissociation. The X-ray crystal structures of NCPs containing the disulfides in isolation and in combination were determined. Both disulfides stabilize the structure of the NCP without disturbing the overall structure. Nucleosomes containing these modifications will be advantageous for biochemical and structural studies as a consequence of their greater resistance to dissociation during high dilution in purification, elevated salt for crystallization and vitrification for cryogenic electron microscopy.


    Organizational Affiliation

    ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zürich, Switzerland. Electronic address: richmond@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2AE135Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2ACG129Xenopus laevisMutation(s): 1 
Gene Names: hist1h2ajLOC494591
Find proteins for P06897 (Xenopus laevis)
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Go to UniProtKB:  P06897
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1DH122Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
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Go to UniProtKB:  P02281
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (147-MER)I147Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (147-MER)J147Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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E, I, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, C, E, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.753α = 90
b = 182.578β = 90
c = 109.645γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references