8JCC

Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA-histone interactions.

Ding, D.Pang, M.Y.H.Deng, M.Nguyen, T.T.Liu, Y.Sun, X.Xu, Z.Zhang, Y.Zhai, Y.Yan, Y.Ishibashi, T.

(2024) Nucleic Acids Res 52: 11612-11625

  • DOI: https://doi.org/10.1093/nar/gkae825
  • Primary Citation of Related Structures:  
    8JBX, 8JCC, 8JCD

  • PubMed Abstract: 

    Multiple testis-specific histone variants are involved in the dynamic chromatin transitions during spermatogenesis. H2B.W1 (previously called H2BFWT) is an H2B variant specific to primate testis with hitherto unclear functions, although its single-nucleotide polymorphisms (SNPs) are closely associated with male non-obstructive infertility. Here, we found that H2B.W1 is only expressed in the mid-late spermatogonia stages, and H2B.W1 nucleosomes are defined by a more flexible structure originating from weakened interactions between histones and DNA. Furthermore, one of its SNPs, H2B.W1-H100R, which is associated with infertility, further destabilizes the nucleosomes and increases the nucleosome unwrapping rate by interfering with the R100 and H4 K91/R92 interaction. Our results suggest that destabilizing H2B.W1 containing nucleosomes might change the chromatin structure of spermatogonia, and that H2B.W1-H100R enhances the nucleosome-destabilizing effects, leading to infertility.


  • Organizational Affiliation

    Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
135Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
PHAROS:  P68431
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UniProt GroupP68431
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Homo 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
PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
129Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
PHAROS:  P04908
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UniProt GroupP04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type W-T
D, H
152Homo sapiensMutation(s): 0 
Gene Names: H2BW1H2BFWT
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z2G1 (Homo sapiens)
Explore Q7Z2G1 
Go to UniProtKB:  Q7Z2G1
GTEx:  ENSG00000123569 
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UniProt GroupQ7Z2G1
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (147-MER)147synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (147-MER)147synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32170548
The University Grants Committee, Research Grants Council (RGC)Hong KongC7009-20G

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references