2CV5

Crystal structure of human nucleosome core particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 

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This is version 1.3 of the entry. See complete history


Literature

Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle

Tsunaka, Y.Kajimura, N.Tate, S.Morikawa, K.

(2005) Nucleic Acids Res 33: 3424-3434

  • DOI: https://doi.org/10.1093/nar/gki663
  • Primary Citation of Related Structures:  
    2CV5

  • PubMed Abstract: 

    Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 A crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location -5.0 to -2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA-DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment.


  • Organizational Affiliation

    Department of Structural Biology, Biomolecular Engineering Research Institute 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1C [auth A],
G [auth E]
136Homo sapiensMutation(s): 0 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]
103Homo sapiensMutation(s): 0 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.aE [auth C],
I [auth G]
130Homo sapiensMutation(s): 0 
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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UniProt GroupP04908
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B KF [auth D],
J [auth H]
126Homo sapiensMutation(s): 0 
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Find proteins for O60814 (Homo sapiens)
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PHAROS:  O60814
GTEx:  ENSG00000197903 
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (146-MER)A [auth I],
B [auth J]
146N/A
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
K [auth I]
L [auth I]
M [auth I]
N [auth J]
O [auth J]
K [auth I],
L [auth I],
M [auth I],
N [auth J],
O [auth J],
P [auth J],
Q [auth J],
R [auth J],
U [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
S [auth A],
T [auth C],
V [auth E],
W [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.564α = 90
b = 108.37β = 90
c = 169.425γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations