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- EMDB-53505: Structure of the H3.V-H4.V variant nucleosome core particle from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53505
TitleStructure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei
Map data
Sample
  • Complex: H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNA
    • Complex: Histone octamer
      • Protein or peptide: Histone H3 variant
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: Widom 601 145 bp DNA
      • DNA: Widom 601 145 bp DNA (115-mer ordered and built)
      • DNA: Widom 601 145 bp DNA (115-mer ordered and built)
Keywordsnucleosome / histone / nucleus / DNA BINDING PROTEIN
Function / homology
Function and homology information


termination of RNA polymerase II transcription / phosphate ion binding / chromosome organization / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / chromosome, telomeric region / protein heterodimerization activity / DNA binding ...termination of RNA polymerase II transcription / phosphate ion binding / chromosome organization / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / chromosome, telomeric region / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4 / Histone H4 / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H3 variant / Histone H2B / Histone H2A / Histone H4
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsDeak G / Wilson MD
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust210493/Z/18/Z United Kingdom
Medical Research Council (MRC, United Kingdom)T029471/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M010996/1 United Kingdom
Wellcome Trust218470 United Kingdom
CitationJournal: Structure / Year: 2026
Title: Trypanosome histone variants H3.V and H4.V promote nucleosome plasticity in repressed chromatin
Authors: Deak G / Burdett H / Watson JA / Wilson MD
History
DepositionApr 26, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53505.png

Downloads & links

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Map

FileDownload / File: emd_53505.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.2981358 - 0.5314877
Average (Standard dev.)0.0003245839 (±0.012448501)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_53505_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53505_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53505_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H3.V-H4.V variant nucleosome core particle from Trypanosoma bruce...

EntireName: H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNA
Components
  • Complex: H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNA
    • Complex: Histone octamer
      • Protein or peptide: Histone H3 variant
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: Widom 601 145 bp DNA
      • DNA: Widom 601 145 bp DNA (115-mer ordered and built)
      • DNA: Widom 601 145 bp DNA (115-mer ordered and built)

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Supramolecule #1: H3.V-H4.V variant nucleosome core particle from Trypanosoma bruce...

SupramoleculeName: H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote)
Molecular weightTheoretical: 89.64 KDa

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Supramolecule #2: Histone octamer

SupramoleculeName: Histone octamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Details: Trypanosoma brucei histone octamer composed of one H4.V-H3.V-H3.V-H4.V tetramer and two H2A-H2B dimers
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote)

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Supramolecule #3: Widom 601 145 bp DNA

SupramoleculeName: Widom 601 145 bp DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote)

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Macromolecule #1: Histone H3 variant

MacromoleculeName: Histone H3 variant / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote) / Strain: TREU927
Molecular weightTheoretical: 15.92058 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AQMKKITPRP VRPKSVASRP IQSVARAPVK KVENTPPQKR HHRWRPGTVA LREIRRLQSS TDFLIQRAPF RRFLREVVSN LKDSYRMSA ACVDAIQEAT ETYITSVFMD ANLCTLHANR VTLFPKDIQL ALKLRGERN

UniProtKB: Histone H3 variant

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote) / Strain: TREU927
Molecular weightTheoretical: 11.150069 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AKGKRVGESK GAQKRQKKVL RDNVRGITRG SIRRLARRAG VKRISGVIYD EVRGVLKTFV ESIVRDAGAY TEYSRKKTVT AAHVVFALR KRGKVLYGYD

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote) / Strain: TREU927
Molecular weightTheoretical: 14.108614 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ATPKQAVKKA SKGGSSRSVK AGLIFPVGRV GTLLRRGQYA RRIGASGAVY MAAVLEYLTA ELLELSVKAA AQQTKKTKRL TPRTVTLAV RHDDDLGALL RNVTMSRGGV MPSLNKALAK KQKSGKHAKA TPSV

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote) / Strain: TREU927
Molecular weightTheoretical: 12.464503 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ATPKSTPAKT RKEAKKTRRQ RKRTWNVYVS RSLRSINSQM SMTSRTMKIV NSFVNDLFER IAAEAATIVR VNRKRTLGAR ELQTAVRLV LPADLAKHAM AEGTKAVSHA SS

UniProtKB: Histone H2B

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Macromolecule #5: Widom 601 145 bp DNA (115-mer ordered and built)

MacromoleculeName: Widom 601 145 bp DNA (115-mer ordered and built) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.99166 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DG) (DA)(DT)

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Macromolecule #6: Widom 601 145 bp DNA (115-mer ordered and built)

MacromoleculeName: Widom 601 145 bp DNA (115-mer ordered and built) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.520383 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG) (DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC4H13Cl2NO3Tris-HCl
30.0 mMNaClsodium chloride
1.0 mMC10H16N2O8EDTA
1.0 mMC4H10O2S2DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
Details: The grids were pretreated with fresh carbon evaporation prior to sample addition.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsCrosslinked with 0.05% glutaraldehyde prior to separation by size exclusion chromatography

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 8052 / Average exposure time: 4.4 sec. / Average electron dose: 54.5 e/Å2
Details: Images were collected in super-resolution mode, with 50 equally dosed total frames recorded
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 83000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 83000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImages were re-gain corrected based on estimated gain from the raw data.
Particle selectionNumber selected: 5780374
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Software - details: Patch CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-Initio Reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 362400
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.6.2)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7ya3

chain_id: C, source_name: AlphaFold, initial_model_type: in silico model

7ya3

chain_id: G, source_name: AlphaFold, initial_model_type: in silico model

8com

chain_id: D, source_name: PDB, initial_model_type: experimental modelchain D from 8COM

89t1

chain_id: H, source_name: AlphaFold, initial_model_type: in silico model

87x7

chain_id: A, source_name: AlphaFold, initial_model_type: in silico model

87x7

chain_id: E, source_name: AlphaFold, initial_model_type: in silico model

87h6

chain_id: B, source_name: AlphaFold, initial_model_type: in silico model

87h6

chain_id: F, source_name: AlphaFold, initial_model_type: in silico model
chain_id: I, source_name: AlphaFold, initial_model_type: in silico modelsynthetic DNA construct
chain_id: J, source_name: AlphaFold, initial_model_type: in silico modelsynthetic DNA construct
RefinementSpace: REAL / Overall B value: 116
Output model

PDB-9r1d:
Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei

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