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- EMDB-55877: HIV-1 capsid hexamers after 3 days post infection without Lenacapavir -

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Basic information

Entry
Database: EMDB / ID: EMD-55877
TitleHIV-1 capsid hexamers after 3 days post infection without Lenacapavir
Map data
SampleHIV-1 != Human immunodeficiency virus type 1 (BRU ISOLATE)

HIV-1

  • Virus: Human immunodeficiency virus type 1 (BRU ISOLATE)
KeywordsHIV-1 / capsid / hexamer / STA / Lenacapavir / VIRUS
Biological speciesHuman immunodeficiency virus type 1 (BRU ISOLATE)
Methodsubtomogram averaging / cryo EM / Resolution: 37.8 Å
AuthorsMourer T / Di Nunzio F / Harastani M / Gazi A / Sartori-Rupp A
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de Recherches Sur le Sida et les Hepatites Virales (ANRS)ECTZ192036 France
Agence Nationale de Recherches Sur le Sida et les Hepatites Virales (ANRS)ECTZ137593 France
CitationJournal: To Be Published
Title: HIV-1 capsid hexamers in presence of LEN
Authors: Mourer T / Di Nunzio F / Harastani M / Gazi A / Sartori-Rupp A
History
DepositionNov 27, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55877.png

Downloads & links

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Map

FileDownload / File: emd_55877.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.9 Å/pix.
x 64 pix.
= 313.6 Å		4.9 Å/pix.
x 64 pix.
= 313.6 Å		4.9 Å/pix.
x 64 pix.
= 313.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.6773542 - 1.7224648
Average (Standard dev.)0.0010708859 (±0.23495606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-31-31-31
Dimensions646464
Spacing646464
CellA=B=C: 313.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55877_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_55877_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_55877_half_map_2.map
Projections & Slices
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Sample components

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Entire : HIV-1

EntireName: HIV-1 (virus)
Components
  • Virus: Human immunodeficiency virus type 1 (BRU ISOLATE)

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Supramolecule #1: Human immunodeficiency virus type 1 (BRU ISOLATE)

SupramoleculeName: Human immunodeficiency virus type 1 (BRU ISOLATE) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11686
Sci species name: Human immunodeficiency virus type 1 (BRU ISOLATE)
Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293.15 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 4.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 37.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: TOM Toolbox / Number subtomograms used: 836
ExtractionNumber tomograms: 10 / Number images used: 836 / Software - Name: TOM Toolbox
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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