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- EMDB-74814: HIV-1 ADA.CM.755* Env (Immature VLPs, tilted class) -

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Basic information

Entry
Database: EMDB / ID: EMD-74814
TitleHIV-1 ADA.CM.755* Env (Immature VLPs, tilted class)
Map dataHIV-1 ADA.CM.755* Env (Immature VLPs, tilted class)
Sample
  • Virus: HIV-1 06TG.HT008 (virus)
    • Protein or peptide: HIV-1 ADA.CM.755* Env
KeywordsHIV-1 / Env / membrane / fusion / VIRAL PROTEIN
Biological speciesHIV-1 06TG.HT008 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 13.6 Å
AuthorsCroft JT / Lee KK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01- AI179697 United States
CitationJournal: bioRxiv / Year: 2026
Title: Structure of HIV-1 Env glycoprotein on virions reveals an alternative fusion subunit organization and native membrane coupling.
Authors: Jacob T Croft / Hung N Do / Daniel P Leaman / Klaus N Lovendahl / Pooja Ralli-Jain / Katelyn J Chase / Chengbo Chen / Vidya Mangala Prasad / Cynthia A Derdeyn / Michael B Zwick / S Gnanakaran / Kelly K Lee /
Abstract: An effective vaccine for Human Immunodeficiency Virus type-1 (HIV-1) has yet to be developed, and detailed characterization of functional Env glycoprotein, the primary antigenic target on virions, ...An effective vaccine for Human Immunodeficiency Virus type-1 (HIV-1) has yet to be developed, and detailed characterization of functional Env glycoprotein, the primary antigenic target on virions, has remained elusive. While engineered Env trimers recapitulate many aspects of functional Env, key differences in antigenicity and dynamic behavior have been reported. Here, cryo-electron tomography and subtomogram averaging of HIV-1 virus-like particles (VLPs) revealed conformational differences in critical membrane-proximal regions compared to soluble Envs. Hydrogen/Deuterium-Exchange Mass Spectrometry and Molecular Dynamics captured dynamic profiles of membrane-bound Env and identified critical interactions with membrane. We show that disruption of the viral membrane results in relaxation of Env to a form that resembles engineered, soluble trimers. Additionally, Env from mature and immature VLPs exhibit only minor conformational differences, while surface clustering on virions changes significantly. These studies provide new insights into the essential role the membrane plays in maintaining Env in its native conformational form.
History
DepositionDec 23, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74814.png

Downloads & links

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Map

FileDownload / File: emd_74814.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 ADA.CM.755* Env (Immature VLPs, tilted class)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.77 Å/pix.
x 112 pix.
= 310.554 Å		2.77 Å/pix.
x 112 pix.
= 310.554 Å		2.77 Å/pix.
x 112 pix.
= 310.554 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7728 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.63
Minimum - Maximum-9.987261 - 9.363353999999999
Average (Standard dev.)0.04415337 (±0.9996328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-56-56
Dimensions112112112
Spacing112112112
CellA=B=C: 310.5536 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HIV-1 ADA.CM.755* Env (Immature VLPs, tilted class) half map 1

Fileemd_74814_half_map_1.map
AnnotationHIV-1 ADA.CM.755* Env (Immature VLPs, tilted class) half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 ADA.CM.755* Env (Immature VLPs, tilted class) half map 2

Fileemd_74814_half_map_2.map
AnnotationHIV-1 ADA.CM.755* Env (Immature VLPs, tilted class) half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 06TG.HT008

EntireName: HIV-1 06TG.HT008 (virus)
Components
  • Virus: HIV-1 06TG.HT008 (virus)
    • Protein or peptide: HIV-1 ADA.CM.755* Env

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Supramolecule #1: HIV-1 06TG.HT008

SupramoleculeName: HIV-1 06TG.HT008 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 587638 / Sci species name: HIV-1 06TG.HT008 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: HIV-1 ADA.CM.755* Env

MacromoleculeName: HIV-1 ADA.CM.755* Env / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: HIV-1 06TG.HT008 (virus)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARTEKLW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEVV LENVTENFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTDLR NVTNSSSEGM RGEIKNCSFN ITTSIRDKVK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARTEKLW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEVV LENVTENFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTDLR NVTNSSSEGM RGEIKNCSFN ITTSIRDKVK KDYALFYRLD VVPIDNDNTS YRLINCNTST ITQACPKVSF EPIPIHYCTP AGFAILKCKD KKFNGTGPCK NVSTVQCTHG IRPVVSTQLL LNGSLAEEEV VIRSSNFTDN AKNIIVQLKE SVEINCTRPN NNTRKSIHIG PGRAFYTTGE IIGDIRQAHC NISRTKWNNT LNQIATKLKE QFGNNKTIVF NQSSGGDPEI VMHSFNCGGE FFYCNSTQLF NSTWNFNGTW NLTQSNGTEG NDTITLPCRI KQIINMWQEV GKAMYAPPIR GQIRCSSNIT GLILTRDGGT NSSGSEIFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTK AKRRVVQREK RAVGTIGAMF LGFLGAAGST MGAASMTLTV QARQLLSGIV QQQNNLLRAI EAQQHLLQLT VWGIRQLQAR VLAVERYLRD QQLLGIWGCS GKLICTTAVP WNASWSNKSL EQIWNNMTWM EWDREINNYT SLIHSLIEEA QNQQEKNEQE LLELDKWASL WNWFNITNWL WYIKLFIMIV GGLVGLRIVF AVLSIVNRVR QGYSPLSFQT HLPTPRGPDR PEGIEEEGGE RDRDRSIRLV NGFLA

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.4 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: 2.0 µm / Nominal magnification: 64000
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: 13.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.99.67) / Number subtomograms used: 23894
ExtractionNumber tomograms: 424 / Number images used: 65438 / Software - Name: EMAN2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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