[English] 日本語
Yorodumi
- EMDB-55943: Structure of the H4.V variant nucleosome core particle from Trypa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55943
TitleStructure of the H4.V variant nucleosome core particle from Trypanosoma brucei
Map dataSharpened map
Sample
  • Complex: H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNA
    • Complex: Histone octamer
      • Protein or peptide: T. brucei Histone H3
      • Protein or peptide: T. brucei Histone H4.V
      • Protein or peptide: T. brucei Histone H2A
      • Protein or peptide: T. brucei Histone H2B
    • Complex: Widom 601 145 bp DNA
      • DNA: Widom 601 145 bp DNA
      • DNA: Widom 601 145 bp DNA
Keywordsnucleosome / histone / nucleus / DNA BINDING PROTEIN
Function / homology
Function and homology information


phosphate ion binding / chromosome organization / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
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 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B / Histone H3, putative / Histone H2A / Histone H4
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsDeak G / Wilson MD
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust210493/Z/18/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M010996/1 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
DepositionDec 4, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55943.png

Downloads & links

-
Map

FileDownload / File: emd_55943.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 320 pix.
= 224. Å		0.7 Å/pix.
x 320 pix.
= 224. Å		0.7 Å/pix.
x 320 pix.
= 224. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0625
Minimum - Maximum-0.11967727 - 0.26152894
Average (Standard dev.)0.0016058547 (±0.0126927495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 224.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_55943_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map

Fileemd_55943_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_55943_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_55943_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : H4.V variant nucleosome core particle from Trypanosoma brucei rec...

EntireName: H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNA
Components
  • Complex: H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNA
    • Complex: Histone octamer
      • Protein or peptide: T. brucei Histone H3
      • Protein or peptide: T. brucei Histone H4.V
      • Protein or peptide: T. brucei Histone H2A
      • Protein or peptide: T. brucei Histone H2B
    • Complex: Widom 601 145 bp DNA
      • DNA: Widom 601 145 bp DNA
      • DNA: Widom 601 145 bp DNA

-
Supramolecule #1: H4.V variant nucleosome core particle from Trypanosoma brucei rec...

SupramoleculeName: 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

-
Supramolecule #2: Histone octamer

SupramoleculeName: Histone octamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote)

-
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)

-
Macromolecule #1: T. brucei Histone H3

MacromoleculeName: T. brucei Histone H3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote) / Strain: TREU927
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SRTKETARTK KTITSKKSKK ASKGSDAASG VKTAQRRWRP GTVALREIRQ FQRSTDLLLQ KAPFQRLVRE VSGAQKEGLR FQSSAILAAQ EATESYIVSL LADTNRACIH SGRVTIQPKD IHLALCLRGE RA

UniProtKB: Histone H3, putative

-
Macromolecule #2: T. brucei Histone H4.V

MacromoleculeName: T. brucei Histone H4.V / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote) / Strain: TREU927
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AKGKRVGESK GAQKRQKKVL RDNVRGITRG SIRRLARRAG VKRISGVIYD EVRGVLKTFV ESIVRDAGAY TEYSRKKTVT AAHVVFALRK RGKVLYGYD

UniProtKB: Histone H4

-
Macromolecule #3: T. brucei Histone H2A

MacromoleculeName: T. brucei Histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote) / Strain: TREU927
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ATPKQAVKKA SKGGSSRSVK AGLIFPVGRV GTLLRRGQYA RRIGASGAVY MAAVLEYLTA ELLELSVKAA AQQTKKTKRL TPRTVTLAVR HDDDLGALLR NVTMSRGGVM PSLNKALAKK QKSGKHAKAT PSV

UniProtKB: Histone H2A

-
Macromolecule #4: T. brucei Histone H2B

MacromoleculeName: T. brucei Histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (eukaryote) / Strain: TREU927
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ATPKSTPAKT RKEAKKTRRQ RKRTWNVYVS RSLRSINSQM SMTSRTMKIV NSFVNDLFER IAAEAATIVR VNRKRTLGAR ELQTAVRLVL PADLAKHAMA EGTKAVSHAS S

UniProtKB: Histone H2B

-
Macromolecule #5: Widom 601 145 bp DNA

MacromoleculeName: Widom 601 145 bp DNA / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATCGATGTAT ATATCTGACA CGTGCCTGGA GACTAGGGAG TAATCCCCTT GGCGGTTAAA ACGCGGGGGA CAGCGCGTAC GTGCGTTTAA GCGGTGCTAG AGCTGTCTAC GACCAATTGA GCGGCCTCGG CACCGGGATT CTGAT

-
Macromolecule #6: Widom 601 145 bp DNA

MacromoleculeName: Widom 601 145 bp DNA / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATCAGAATCC CGGTGCCGAG GCCGCTCAAT TGGTCGTAGA CAGCTCTAGC ACCGCTTAAA CGCACGTACG CGCTGTCCCC CGCGTTTTAA CCGCCAAGGG GATTACTCCC TAGTCTCCAG GCACCTGTCA GATATATACA TCGAT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.07 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: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsCrosslinked with 0.1% glutaraldehyde

-
Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 10414 / Average exposure time: 3.69 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 1039631
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Software - details: patch CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-Initio Reconstruction
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Software - details: homogeneous refinement / Number images used: 58216
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final 3D classificationNumber classes: 50 / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementOverall B value: 113.4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more