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- EMDB-55448: In situ structure of the H1-bound nucleosome in stacking nucleosomes -

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Basic information

Entry
Database: EMDB / ID: EMD-55448
TitleIn situ structure of the H1-bound nucleosome in stacking nucleosomes
Map data
Sample
  • Cell: Permeabilised and supplemented CEM T cells
KeywordsNucleosome / Histone H1 / H1-bound di-nucleosome / chromatosome / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 9.9 Å
AuthorsHou Z / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust311427/Z/24/Z (P.Z.) United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: chromatin dynamics and HIV-1 nuclear trafficking.
Authors: Zhen Hou / Yao Shen / Long Chen / Juan Shen / David I Stuart / Peijun Zhang /
Abstract: The organization and dynamics of chromatin within intact nuclei remain poorly defined, limiting understanding of how nuclear architecture influences macromolecular transport. HIV-1 provides a ...The organization and dynamics of chromatin within intact nuclei remain poorly defined, limiting understanding of how nuclear architecture influences macromolecular transport. HIV-1 provides a striking example of a large complex that must traverse this dynamic landscape to access integration sites within transcriptionally active regions. Here, we combine a functional nuclear import system with correlative cryo-electron tomography to visualize chromatin architecture and HIV-1 cores during nuclear penetration. Native nucleosomes resolved at 5.6 Å reveal four structural classes, from compact conformations at the nuclear periphery to open, flexible forms in the interior, defining a spatially heterogeneous and dynamic chromatin landscape. Within this environment, HIV-1 cores decorated with nuclear factors exclude nearby nucleosomes and preferentially associate with open chromatin. Disruption of CPSF6-capsid interactions abolishes these associations, confining viral cores to peripheral chromatin. These findings establish an framework linking chromatin structure and dynamics to HIV-1 nuclear trafficking and provide a structural basis for viral navigation within the dynamic nuclear landscape.
History
DepositionOct 21, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55448.png

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Map

FileDownload / File: emd_55448.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.94 Å/pix.
x 144 pix.
= 279.36 Å		1.94 Å/pix.
x 144 pix.
= 279.36 Å		1.94 Å/pix.
x 144 pix.
= 279.36 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.94 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 25.699999999999999
Minimum - Maximum-64.103769999999997 - 113.976973999999998
Average (Standard dev.)0.4462772 (±4.5764556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 279.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55448_msk_1.map
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Half map: #1

Fileemd_55448_half_map_1.map
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Half map: #2

Fileemd_55448_half_map_2.map
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Sample components

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Entire : Permeabilised and supplemented CEM T cells

EntireName: Permeabilised and supplemented CEM T cells
Components
  • Cell: Permeabilised and supplemented CEM T cells

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Supramolecule #1: Permeabilised and supplemented CEM T cells

SupramoleculeName: Permeabilised and supplemented CEM T cells / type: cell / ID: 1 / Parent: 0
Details: CEM T cells are permeabilised with 0.018% digitonin and supplemented with rabbit reticulocyte lysate + ATP + GTP + creatine phosphate + creatine kinase
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 310.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 18563
ExtractionNumber tomograms: 253 / Number images used: 673750 / Software - Name: emClarity (ver. 1.5.0.2)
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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