8COM

Structure of the Nucleosome Core Particle from Trypanosoma brucei


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Histone divergence in trypanosomes results in unique alterations to nucleosome structure.

Deak, G.Wapenaar, H.Sandoval, G.Chen, R.Taylor, M.R.D.Burdett, H.Watson, J.A.Tuijtel, M.W.Webb, S.Wilson, M.D.

(2023) Nucleic Acids Res 51: 7882-7899

  • DOI: https://doi.org/10.1093/nar/gkad577
  • Primary Citation of Related Structures:  
    8COM

  • PubMed Abstract: 

    Eukaryotes have a multitude of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically and structurally characterised nucleosome core particles (NCPs) from the kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened overall DNA binding. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.


  • Organizational Affiliation

    Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3, putative
A, E
132Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: TB927.1.2430TB927.1.2450TB927.1.2470TB927.1.2490TB927.1.2510TB927.1.2530TB927.1.2550
UniProt
Find proteins for Q4GYX7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Go to UniProtKB:  Q4GYX7
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UniProt GroupQ4GYX7
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
99Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q57Z31 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Go to UniProtKB:  Q57Z31
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UniProt GroupQ57Z31
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
133Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q57YA3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Go to UniProtKB:  Q57YA3
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UniProt GroupQ57YA3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
111Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q389T1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q389T1 
Go to UniProtKB:  Q389T1
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UniProt GroupQ389T1
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Entity ID: 5
MoleculeChains LengthOrganismImage
Widom 601 145 bp DNA (127-mer ordered and built)145synthetic construct
Sequence Annotations
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Entity ID: 6
MoleculeChains LengthOrganismImage
Widom 601 145 bp DNA (127-mer ordered and built)145synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210493
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M010996/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references