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- EMDB-75641: Full-length BG505 HIV-1 Env expressed in VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-75641
TitleFull-length BG505 HIV-1 Env expressed in VLP
Map dataFull length BG505 HIV-1 Envelope glycoprotein expressed in eVLPs.
Sample
  • Virus: Human immunodeficiency virus 1
Keywordsenvelope glycoprotein / HIV-1 Env / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsDuquette M / Villa E
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI179188 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50-AI150464 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2026
Title: N-Glycans modulate tilting of HIV-1 envelope glycoprotein.
Authors: Mohamed Shehata / Lorenzo Casalino / Madeleine Duquette / Siyu Chen / Alex Flaherty / Patrick M Waller / Elizabeth Villa / Rommie E Amaro /
Abstract: Human immunodeficiency virus-1 (HIV-1) remains a global health crisis, with over 40 million people living with the virus and no effective vaccine available. Central to HIV infection and immune ...Human immunodeficiency virus-1 (HIV-1) remains a global health crisis, with over 40 million people living with the virus and no effective vaccine available. Central to HIV infection and immune evasion is the envelope glycoprotein (Env), a heavily glycosylated class I fusion protein that mediates viral entry and is the sole immunogenic target. Despite the recent advancements provided by imaging techniques, the characterization of Env's structure and dynamics within its native membrane environment remains incomplete. Here, we present microsecond-long, all-atom molecular dynamics simulations of the full-length, glycosylated Env glycoprotein embedded in a biologically relevant lipid bilayer. Our simulations, corroborated by cryo-electron tomography, reveal a pronounced tilting motion of Env relative to the membrane. Importantly, we identify a critical role for N-linked glycans at N88 and N611 in modulating the transition to tilted conformations. Alongside illuminating the sites of vulnerability within the glycan shield, the results presented here underscore Env tilting dynamics as a feature that can be leveraged in immunogen design.
History
DepositionFeb 18, 2026-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75641.png

Downloads & links

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Map

FileDownload / File: emd_75641.map.gz / Format: CCP4 / Size: 489.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull length BG505 HIV-1 Envelope glycoprotein expressed in eVLPs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.24 Å/pix.
x 50 pix.
= 312.2 Å		6.24 Å/pix.
x 50 pix.
= 312.2 Å		6.24 Å/pix.
x 50 pix.
= 312.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.244 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-1.0575483 - 1.1771443
Average (Standard dev.)0.002832769 (±0.10659066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions505050
Spacing505050
CellA=B=C: 312.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_75641_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75641_half_map_2.map
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 / Sci species strain: BG505 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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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 / Details: 1xPBS
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.78 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.4) / Number subtomograms used: 4396
ExtractionNumber tomograms: 261 / Number images used: 6389 / Software - Name: RELION (ver. 3.1.4)
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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