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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 / nucleosome / heterochromatin formation / 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 / nucleosome / heterochromatin formation / nucleosome assembly / chromosome, telomeric region / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2A conserved site / Histone H2A signature. / Histone H2B 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: Gauri Deák / Hayden Burdett / James A Watson / Marcus D Wilson /
Abstract: Histone variants define distinct chromatin states by modulating the biophysical properties of nucleosomes. Variants play a particularly important role in the parasitic protist Trypanosoma brucei, ...Histone variants define distinct chromatin states by modulating the biophysical properties of nucleosomes. Variants play a particularly important role in the parasitic protist Trypanosoma brucei, which has unusual chromatin and lacks a canonical repressive heterochromatin system. Instead, T. brucei utilizes specialized divergent histone variants H3.V and H4.V. However, the biochemical basis of their repressive functions is unknown. Here, we determined the structure of the H3.V-H4.V nucleosome core particle and biochemically characterized variant-containing nucleosomes and nucleosome arrays, probing their unique properties. We discovered that surprisingly for repressive-state nucleosomes, H3.V promotes pronounced DNA splaying, largely via its N-terminal tail region, while retaining overall stability that is comparable to canonical nucleosomes. In contrast, H4.V exhibits near-identical binding to DNA but mediates a slight increase in histone octamer stability. The surface of the H3.V-H4.V nucleosome is altered and provides a differential platform for chromatin-binding proteins, linking the variants to parasite pathogenicity.
History
DepositionApr 26, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 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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