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

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Basic information

Entry
Database: PDB / ID: 9r1d
TitleStructure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei
Components
  • (Widom 601 145 bp DNA (115-mer ordered and ...) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3 variant
  • Histone H4
KeywordsDNA BINDING PROTEIN / nucleosome / histone / nucleus
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
DNA / DNA (> 10) / DNA (> 100) / Histone H3 variant / Histone H2B / Histone H2A / Histone H4
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsDeak, G. / Wilson, M.D.
Funding support United Kingdom, 4items
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, J.A. / Wilson, M.D.
History
DepositionApr 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3 variant
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3 variant
F: Histone H4
G: Histone H2A
H: Histone H2B
I: Widom 601 145 bp DNA (115-mer ordered and built)
J: Widom 601 145 bp DNA (115-mer ordered and built)


Theoretical massNumber of molelcules
Total (without water)196,80010
Polymers196,80010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3 variant


Mass: 15920.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: TREU927 / Gene: Tb10.61.1090 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q387X7
#2: Protein Histone H4


Mass: 11150.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: TREU927 / Gene: 10C8.135, Tb927.2.2670 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q587H6
#3: Protein Histone H2A


Mass: 14108.614 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: TREU927
Gene: 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, ...Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q57YA3
#4: Protein Histone H2B


Mass: 12464.503 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: TREU927
Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q389T1

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Widom 601 145 bp DNA (115-mer ordered and ... , 2 types, 2 molecules IJ

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


Mass: 44991.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain Widom 601 145 bp DNA (115-mer ordered and built)


Mass: 44520.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNACOMPLEXall0RECOMBINANT
2Histone octamerCOMPLEX#1-#41RECOMBINANTTrypanosoma brucei histone octamer composed of one H4.V-H3.V-H3.V-H4.V tetramer and two H2A-H2B dimers
3Widom 601 145 bp DNACOMPLEX#5-#61RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.1967 MDaNO
210.1071 MDaNO
310.08964 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Trypanosoma brucei brucei TREU927 (eukaryote)185431
32Trypanosoma brucei brucei TREU927 (eukaryote)185431
43Trypanosoma brucei brucei TREU927 (eukaryote)185431
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris-HClC4H13Cl2NO31
230 mMsodium chlorideNaCl1
31 mMEDTAC10H16N2O81
41 mMDTTC4H10O2S21
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Crosslinked with 0.05% glutaraldehyde prior to separation by size exclusion chromatography
Specimen supportDetails: The grids were pretreated with fresh carbon evaporation prior to sample addition.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 83000 X / Calibrated magnification: 83000 X / Nominal defocus max: 3300 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K
Image recordingAverage exposure time: 4.4 sec. / Electron dose: 54.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8052
Details: Images were collected in super-resolution mode, with 50 equally dosed total frames recorded
Image scansSampling size: 5 µm / Width: 4092 / Height: 5760

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.6.2particle selectionManual picking followed by Template-Based Picking
2EPUimage acquisition
4cryoSPARC4.6.2CTF correctionPatch CTF correction
7UCSF ChimeraX1.7.1model fitting
9cryoSPARC4.6.2initial Euler assignment
10cryoSPARC4.6.2final Euler assignment
11cryoSPARC4.6.2classification
12cryoSPARC4.6.23D reconstruction
19PHENIX1.21.1model refinement
20Coot0.9.8.7model refinement
21ISOLDE1.7.1model refinement
22UCSF ChimeraX1.7.1model refinement
Image processingDetails: Images were re-gain corrected based on estimated gain from the raw data.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5780374
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 362400 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 116 / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-IDSource nameTypeDetails
1Q57YA3C1AlphaFoldin silico model
2Q57YA3G1AlphaFoldin silico model
38COM

8com

D8COMD2PDBexperimental modelchain D from 8COM
4Q389T1H3AlphaFoldin silico model
5Q387X7A4AlphaFoldin silico model
6Q387X7E4AlphaFoldin silico model
7Q587H6B5AlphaFoldin silico model
8Q587H6F5AlphaFoldin silico model
9IAlphaFoldin silico modelsynthetic DNA construct
10JAlphaFoldin silico modelsynthetic DNA construct

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