6KVD

Crystal structure of human nucleosome containing H2A.J


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Biochemical and structural analyses of the nucleosome containing human histone H2A.J.

Tanaka, H.Sato, S.Koyama, M.Kujirai, T.Kurumizaka, H.

(2020) J Biochem 167: 419-427

  • DOI: 10.1093/jb/mvz109
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Histone H2A.J, a histone H2A variant conserved in mammals, may function in the expression of genes related to inflammation and cell proliferation. In the present study, we purified the human histone H2A.J variant, and found that H2A.J is efficiently ...

    Histone H2A.J, a histone H2A variant conserved in mammals, may function in the expression of genes related to inflammation and cell proliferation. In the present study, we purified the human histone H2A.J variant, and found that H2A.J is efficiently incorporated into the nucleosome in vitro. H2A.J formed the stable nucleosome, which accommodated the DNA ends. Mutations in the H2A.J-specific residues did not affect the nucleosome stability, although the mutation of the H2A.J Ala40 residue, which is conserved in some members of the canonical H2A class, reduced the nucleosome stability. Consistently, the crystal structure of the H2A.J nucleosome revealed that the H2A.J-specific residues, including the Ala40 residue, did not affect the nucleosome structure. These results provide basic information for understanding the function of the H2A.J nucleosome.


    Organizational Affiliation

    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1A, E139Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-JD, H129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
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PHAROS  P06899
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4B, F106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
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PHAROS  P62805
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.JC, G132Homo sapiensMutation(s): 0 
Gene Names: H2AFJH2AJ
Find proteins for Q9BTM1 (Homo sapiens)
Explore Q9BTM1 
Go to UniProtKB:  Q9BTM1
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PHAROS  Q9BTM1
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (146-MER)I, J146Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.64α = 90
b = 108.791β = 90
c = 171.177γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP17H01408
Japan Society for the Promotion of ScienceJapanJP18H05534
Japan Society for the Promotion of ScienceJapanJP18K14677
Japan Society for the Promotion of ScienceJapanJP19K21177
Japan Society for the Promotion of ScienceJapanJP19K06609
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101076
Japan Science and TechnologyJapanJPMJCR16G1
Japan Society for the Promotion of ScienceJapanJP18J13668

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references