8ZVY | pdb_00008zvy

Alpha-Synuclein with H2a-H2b dimer complex structure.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structural and functional insights into the nuclear role of Parkinson's disease-associated alpha-synuclein as a histone chaperone.

Jos, S.Kambaru, A.Prasad, T.K.Parthasarathi, S.Kamariah, N.Nath, S.Padmanabhan, B.Padavattan, S.

(2025) Commun Biol 8: 712-712

  • DOI: https://doi.org/10.1038/s42003-025-08138-0
  • Primary Citation of Related Structures:  
    8ZVY

  • PubMed Abstract: 

    α-Synuclein (αSyn) plays a critical role in the pathogenesis of 'Synucleinopathies'. Although increased nuclear αSyn localization induces neurotoxicity, its definitive physiological role remains elusive. Previous studies on nuclear αSyn are limited to its interactions with individual histones and dsDNA, leaving a significant gap in understanding its interactions with assembled histone H2a-H2b dimer and (H3-H4) 2 tetramer, as well as its role in chromatin regulation. Here, we demonstrate that αSyn binds specifically to both H2a-H2b and (H3-H4) 2 with high affinity. Truncation studies reveal that αSyn(1-103) region interacts with (H3-H4) 2 , while the acidic (121-140) C-terminal end is crucial for H2a-H2b binding and contains a conserved DEF/YxP motif present in other dimer-binding histone chaperones. High-resolution structure of αSyn(121-140) with H2a-H2b complex reveals that αSyn adopts two binding modes (BM-1 and BM-2). Nonetheless, the αSyn C-terminal end in both modes overlap but runs in opposite orientations, specifically interacting with the H2a-L2 and H2b-L1 loop regions of the dimer and cap the H2a-R78 residue. Mutational analysis confirms that αSyn-Y136 and P138 residues, part of the DEF/YxP motif, together with H2a-R78, are critical for αSyn-(H2a-H2b) interaction. The chaperoning assay supports αSyn's function as a histone chaperone, suggesting the potential role of αSyn in the nucleosome assembly/disassembly process.


  • Organizational Affiliation
    • Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1,Histone H2A type 1
A, B
186Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
Go to UniProtKB:  P06897
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP02281P06897
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 1 of Alpha-synuclein
C, D
20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P37840 (Homo sapiens)
Explore P37840 
Go to UniProtKB:  P37840
PHAROS:  P37840
GTEx:  ENSG00000145335 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37840
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.005α = 90
b = 68.24β = 90
c = 102.576γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaECR/2018/002219

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release