5GT3

Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b

Padavattan, S.Thiruselvam, V.Shinagawa, T.Hasegawa, K.Kumasaka, T.Ishii, S.Kumarevel, T.

(2017) Biophys Chem 221: 41-48

  • DOI: 10.1016/j.bpc.2016.11.013
  • Primary Citation of Related Structures:  
    5GT3, 5GSU, 5GT0

  • PubMed Abstract: 
  • Th2a and Th2b are the testis-specific histone variants highly expressed during spermatogenesis. Approximately 4% of the genome is retained in nucleosomes in mature human sperm, which is enriched at loci of developmental importance. Our recent studies ...

    Th2a and Th2b are the testis-specific histone variants highly expressed during spermatogenesis. Approximately 4% of the genome is retained in nucleosomes in mature human sperm, which is enriched at loci of developmental importance. Our recent studies revealed that the mouse histone variant homologs TH2a and TH2b are involved in reprogramming. In the present work, we report three nucleosome structures (NCPs) with human testis-specific histone variants hTh2a and hTh2b, [hGcH (hTh2a-hTh2b-H3-H4), hGcHV1 (hTh2a-H2b-H3-H4) and hGcHV2 (H2a-hTh2b-H3-H4)] and a 146-base pair (bp) duplex DNA fragment at ~3.0Å resolutions. These crystal structures revealed two major changes within the nucleosomes, either with hTh2a, hTh2b or both variants, as compared to the canonical counterpart. First, the H-bonding interactions between the L1-L1' interfaces mediated by the hTh2a/hTh2a' L1-loops are lost. Second, the histone dimer-DNA contacts are considerably reduced, and these changes are localized around ±31 to 35-bp from the nucleosome entry/exit sites. Thus, the modified functional residues at the N- and C-terminal ends of histone variants are responsible for the observed structural changes and regulate the gene expression through specific structural alterations in the chromatin by modulating the chromatin-associated binding proteins.


    Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Structural Biology Laboratory, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan. Electronic address: kumarevel.thirumananseri@riken.jp.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF102Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-DCG129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ADH2AFGH2AC7
Find proteins for P20671 (Homo sapiens)
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PHAROS  P20671
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-ADH126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BATSH2BH2BC1
Find proteins for Q96A08 (Homo sapiens)
Explore Q96A08 
Go to UniProtKB:  Q96A08
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PHAROS  Q96A08
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1AE135Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
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PHAROS  P68431
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
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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E, G, I, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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I, J
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.887α = 90
b = 110.078β = 90
c = 182.811γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection