2PYO

Drosophila nucleosome core

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer.

Clapier, C.R., Chakravarthy, S., Petosa, C., Fernandez-Tornero, C., Luger, K., Muller, C.W.

(2007) Proteins 71: 1-7

  • DOI: https://doi.org/10.1002/prot.21720
  • Primary Citation of Related Structures:  
    2PYO

  • PubMed Abstract: 

    • We determined the 2.45 A crystal structure of the nucleosome core particle from Drosophila melanogaster and compared it to that of Xenopus laevis bound to the identical 147 base-pair DNA fragment derived from human alpha-satellite DNA. Differences between the two structures primarily reflect 16 amino acid substitutions between species, 15 of which are in histones H2A and H2B ...

    We determined the 2.45 A crystal structure of the nucleosome core particle from Drosophila melanogaster and compared it to that of Xenopus laevis bound to the identical 147 base-pair DNA fragment derived from human alpha-satellite DNA. Differences between the two structures primarily reflect 16 amino acid substitutions between species, 15 of which are in histones H2A and H2B. Four of these involve histone tail residues, resulting in subtly altered protein-DNA interactions that exemplify the structural plasticity of these tails. Of the 12 substitutions occurring within the histone core regions, five involve small, solvent-exposed residues not involved in intraparticle interactions. The remaining seven involve buried hydrophobic residues, and appear to have coevolved so as to preserve the volume of side chains within the H2A hydrophobic core and H2A-H2B dimer interface. Thus, apart from variations in the histone tails, amino acid substitutions that differentiate Drosophila from Xenopus histones occur in mutually compensatory combinations. This highlights the tight evolutionary constraints exerted on histones since the vertebrate and invertebrate lineages diverged.

    Organizational Affiliation: 

    European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3C [auth A],
G [auth E]		135Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P02299 (Drosophila melanogaster)
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UniProt GroupP02299
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]		102Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P84040 (Drosophila melanogaster)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G]		120Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P84051 (Drosophila melanogaster)
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UniProt GroupP84051
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BF [auth D],
J [auth H]		122Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P02283 (Drosophila melanogaster)
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UniProt GroupP02283
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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
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K [auth I],
L [auth I],
M [auth I],
N [auth I],
O [auth I],
K [auth I],
L [auth I],
M [auth I],
N [auth I],
O [auth I],
P [auth I],
Q [auth I],
R [auth J],
S [auth J],
T [auth J],
U [auth J],
V [auth J],
W [auth J],
Z [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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AA [auth E],
BA [auth H],
X [auth A],
Y [auth D]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.03α = 90
b = 182.04β = 90
c = 109.42γ = 90
Software Package:
Software NamePurpose
XSCALEdata processing
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance