5AY8

Crystal structure of human nucleosome containing H3.Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and function of human histone H3.Y nucleosome

Kujirai, T.Horikoshi, N.Sato, K.Maehara, K.Machida, S.Osakabe, A.Kimura, H.Ohkawa, Y.Kurumizaka, H.

(2016) Nucleic Acids Res 44: 6127-6141

  • DOI: https://doi.org/10.1093/nar/gkw202
  • Primary Citation of Related Structures:  
    5AY8

  • PubMed Abstract: 

    Histone H3.Y is a primate-specific, distant H3 variant. It is evolutionarily derived from H3.3, and may function in transcription regulation. However, the mechanism by which H3.Y regulates transcription has not been elucidated. In the present study, we determined the crystal structure of the H3.Y nucleosome, and found that many H3.Y-specific residues are located on the entry/exit sites of the nucleosome. Biochemical analyses revealed that the DNA ends of the H3.Y nucleosome were more flexible than those of the H3.3 nucleosome, although the H3.Y nucleosome was stable in vitro and in vivo Interestingly, the linker histone H1, which compacts nucleosomal DNA, appears to bind to the H3.Y nucleosome less efficiently, as compared to the H3.3 nucleosome. These characteristics of the H3.Y nucleosome are also conserved in the H3.Y/H3.3 heterotypic nucleosome, which may be the predominant form in cells. In human cells, H3.Y preferentially accumulated around transcription start sites (TSSs). Taken together, H3.Y-containing nucleosomes around transcription start sites may form relaxed chromatin that allows transcription factor access, to regulate the transcription status of specific genes.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H3.Y
A, E
139Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0DPK2 (Homo sapiens)
Explore P0DPK2 
Go to UniProtKB:  P0DPK2
GTEx:  ENSG00000269466 
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UniProt GroupP0DPK2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
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Go to UniProtKB:  P62805
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UniProt GroupP62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
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Find proteins for P04908 (Homo sapiens)
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UniProt GroupP04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
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Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (146-MER)
I, J
146Homo sapiens
Sequence Annotations
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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 A]
L [auth G]
M [auth I]
N [auth I]
O [auth J]
K [auth A],
L [auth G],
M [auth I],
N [auth I],
O [auth J],
P [auth J],
Q [auth J],
R [auth J]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
S [auth J],
T [auth J]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.522α = 90
b = 101.922β = 90
c = 175.736γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and TechnologyJapan25116002
Platform for Drug Discovery, Informatics, and Structural Life ScienceJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description