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- EMDB-75662: STA of Capsid Protein from Gag VLPs derived from NL4.3 Plasmid -

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Basic information

Entry
Database: EMDB / ID: EMD-75662
TitleSTA of Capsid Protein from Gag VLPs derived from NL4.3 Plasmid
Map dataSTA of Gag VLP Capsid Protein
Sample
  • Virus: Human immunodeficiency virus 1
KeywordsCapsid / Strucural / Lattice / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 6.3 Å
AuthorsPreece B / Saffarian S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56AI150474-06A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R01AI186663 United States
CitationJournal: bioRxiv / Year: 2025
Title: Cryo-ET Reveals Distinct Gag Lattice Architectures in Virus-like Particles and Immature HIV-1.
Authors: Benjamin Preece / Wiley Peppel / Haley Durden / Rodrigo Gallegos / Gabriel Clinger / Nicole Bohn / Antje Huwendiek-Poser / Gillian Ysassi / Allyson Roman / Giovanna Garcia / Tasheena Cly / ...Authors: Benjamin Preece / Wiley Peppel / Haley Durden / Rodrigo Gallegos / Gabriel Clinger / Nicole Bohn / Antje Huwendiek-Poser / Gillian Ysassi / Allyson Roman / Giovanna Garcia / Tasheena Cly / David Belnap / Saveez Saffarian
Abstract: HIV-1 is released from infected cells as immature virions whose membranes are supported by a Gag lattice. During maturation, this lattice is cleaved by the viral protease to release capsid proteins ...HIV-1 is released from infected cells as immature virions whose membranes are supported by a Gag lattice. During maturation, this lattice is cleaved by the viral protease to release capsid proteins that assemble into the mature core. The architecture of the Gag lattice is central to this process, and the Gag lattice is targeted by maturation inhibitors that block cleavage. Using cryo-electron tomography, we compared Gag-only virus-like particles (VLPs) with immature HIV-1 virions and found that VLPs assemble denser and more complete lattices, exhibiting a strong correlation between lattice curvature and Gag copy number. In contrast, immature virions incorporate fewer Gag molecules and display weaker coupling between curvature and Gag stoichiometry. These findings show that while Gag alone can form the canonical immature lattice, additional viral components fine-tune lattice organization and curvature, potentially regulating protease accessibility, virion release, and the onset of HIV-1 maturation.
History
DepositionFeb 20, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75662.png

Downloads & links

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Map

FileDownload / File: emd_75662.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSTA of Gag VLP Capsid Protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 192 pix.
= 270.144 Å		1.41 Å/pix.
x 192 pix.
= 270.144 Å		1.41 Å/pix.
x 192 pix.
= 270.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.407 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0292
Minimum - Maximum-0.08072582 - 0.06419955
Average (Standard dev.)0.00013092399 (±0.011727734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 270.14398 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_75662_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_75662_half_map_2.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
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

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo (ver. 1.1.532) / Number subtomograms used: 29860
ExtractionNumber tomograms: 12 / Number images used: 15400 / Software - Name: Dynamo (ver. 1.1.532)
CTF correctionSoftware - Name: IMOD (ver. 4)
Software - details: Used for CTF Correction and tomographic reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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