5ONG

X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 

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:  
    5OMX, 5ONG, 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 crosslinking the two H2A/H2B heterodimers together to stabilize the histone octamer against H2A/H2B dimer dissociation ...

    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 H3.2C [auth A],
G [auth E]
135Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G]
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1F [auth D],
J [auth H]
122Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (147-MER)A [auth I]147Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (147-MER)B [auth J]147Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth J],
BA [auth J],
CA [auth J],
FA [auth E],
K [auth I],
AA [auth J],
BA [auth J],
CA [auth J],
FA [auth E],
K [auth I],
L [auth I],
M [auth I],
N [auth I],
O [auth I],
P [auth I],
Q [auth I],
R [auth I],
S [auth I],
T [auth I],
U [auth J],
V [auth J],
W [auth J],
X [auth J],
Y [auth J],
Z [auth J]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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DA [auth A],
EA [auth D],
GA [auth E],
HA [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.24α = 90
b = 183.13β = 90
c = 109.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Louis Jeantet PrizeSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references