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- EMDB-55441: In situ structure of wild-type HIV-1 CA hexamer prior to nuclear ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55441
TitleIn situ structure of wild-type HIV-1 CA hexamer prior to nuclear import
Map data
Sample
  • Complex: HIV-1 CA hexamer on native WT viral core
KeywordsHIV-1 / Capsid / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 10.1 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_55441.png

Downloads & links

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Map

FileDownload / File: emd_55441.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.94 Å/pix.
x 128 pix.
= 248.32 Å		1.94 Å/pix.
x 128 pix.
= 248.32 Å		1.94 Å/pix.
x 128 pix.
= 248.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.199999999999999
Minimum - Maximum-35.738334999999999 - 55.650364000000003
Average (Standard dev.)0.000000000288192 (±5.3221626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 248.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55441_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_55441_half_map_2.map
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Sample components

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Entire : HIV-1 CA hexamer on native WT viral core

EntireName: HIV-1 CA hexamer on native WT viral core
Components
  • Complex: HIV-1 CA hexamer on native WT viral core

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Supramolecule #1: HIV-1 CA hexamer on native WT viral core

SupramoleculeName: HIV-1 CA hexamer on native WT viral core / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 150 KDa

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 6404
ExtractionNumber tomograms: 73 / Number images used: 12305 / 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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