9R1D | pdb_00009r1d

Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei

• PDB DOI: https://doi.org/10.2210/pdb9R1D/pdb
• EM Map EMD-53505: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Trypanosoma brucei brucei TREU927, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-26 Released: 2026-01-28 
• Deposition Author(s): Deak, G., Wilson, M.D.
• Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom), Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental

Literature

Trypanosome histone variants H3.V and H4.V promote nucleosome plasticity in repressed chromatin

Deak, G., Burdett, H., Watson, J.A., Wilson, M.D.

(2026) Structure 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 196.8 kDa 
• Atom Count: 9,880 
• Modeled Residue Count: 889 
• Deposited Residue Count: 1,252 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3 variant	A, E	138	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb10.61.1090
UniProt
Find proteins for Q387X7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q387X7  Go to UniProtKB:  Q387X7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	99	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: 10C8.135, Tb927.2.2670
UniProt
Find proteins for Q587H6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q587H6  Go to UniProtKB:  Q587H6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	133	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names:  Tb07.13M20.520, Tb07.13M20.510, Tb07.13M20.530, Tb07.13M20.540, Tb07.13M20.550, Tb07.13M20.560, Tb07.13M20.570, Tb07.13M20.580, Tb07.13M20.590, Tb07.13M20.600, Tb07.13M20.610, Tb07.13M20.620, Tb07.13M20.630, Tb927.7.2820, Tb927.7.2830, Tb927.7.2840, Tb927.7.2850, Tb927.7.2860, Tb927.7.2870, Tb927.7.2880, Tb927.7.2890, Tb927.7.2900, Tb927.7.2910, Tb927.7.2920, Tb927.7.2930, Tb927.7.2940
UniProt
Find proteins for Q57YA3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q57YA3  Go to UniProtKB:  Q57YA3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	111	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names:  Tb10.406.0330, Tb10.406.0350, Tb10.406.0360, Tb10.406.0370, Tb10.406.0380, Tb10.406.0400, Tb10.406.0410, Tb10.406.0420, Tb10.406.0430, Tb10.406.0440, Tb10.406.0450, Tb10.406.0460
UniProt
Find proteins for Q389T1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q389T1  Go to UniProtKB:  Q389T1

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Widom 601 145 bp DNA (115-mer ordered and built)	I	145	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Widom 601 145 bp DNA (115-mer ordered and built)	J	145	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	PHENIX	1.21.1
MODEL REFINEMENT	Coot	0.9.8.7
MODEL REFINEMENT	ISOLDE	1.7.1
MODEL REFINEMENT	UCSF ChimeraX	1.7.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Deak, G., Wilson, M.D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	210493/Z/18/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	T029471/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M010996/1
Wellcome Trust	United Kingdom	218470

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release