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- EMDB-74786: HIV-1 Env BG505.SOSIP -

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Basic information

Entry
Database: EMDB / ID: EMD-74786
TitleHIV-1 Env BG505.SOSIP
Map dataHIV-1 Env BG505.SOSIP
Sample
  • Virus: HIV-1 06TG.HT008 (virus)
    • Protein or peptide: HIV-1 Env BG505.SOSIP
KeywordsHIV-1 / Env / membrane / fusion / VIRAL PROTEIN
Biological speciesHIV-1 06TG.HT008 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 8.0 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_74786.png

Downloads & links

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Map

FileDownload / File: emd_74786.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 Env BG505.SOSIP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.72 Å/pix.
x 84 pix.
= 312.48 Å		3.72 Å/pix.
x 84 pix.
= 312.48 Å		3.72 Å/pix.
x 84 pix.
= 312.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.95
Minimum - Maximum-11.009980000000001 - 23.085985000000001
Average (Standard dev.)0.062368505 (±0.9626675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-42-42-42
Dimensions848484
Spacing848484
CellA=B=C: 312.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HIV-1 Env BG505.SOSIP half map 1

Fileemd_74786_half_map_1.map
AnnotationHIV-1 Env BG505.SOSIP half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 Env BG505.SOSIP half map 2

Fileemd_74786_half_map_2.map
AnnotationHIV-1 Env BG505.SOSIP 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 Env BG505.SOSIP

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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 Env BG505.SOSIP

MacromoleculeName: HIV-1 Env BG505.SOSIP / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: HIV-1 06TG.HT008 (virus)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEIH LENVTEEFNM WKNNMVEQMH TDIISLWDQS LKPCVKLTPL CVTLQCTNVT NNITDDMRGE LKNCSFNMTT ELRDKKQKVY ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEIH LENVTEEFNM WKNNMVEQMH TDIISLWDQS LKPCVKLTPL CVTLQCTNVT NNITDDMRGE LKNCSFNMTT ELRDKKQKVY SLFYRLDVVQ INENQGNRSN NSNKEYRLIN CNTSAITQAC PKVSFEPIPI HYCAPAGFAI LKCKDKKFNG TGPCPSVSTV QCTHGIKPVV STQLLLNGSL AEEEVMIRSE NITNNAKNIL VQFNTPVQIN CTRPNNNTRK SIRIGPGQAF YATGDIIGDI RQAHCNVSKA TWNETLGKVV KQLRKHFGNN TIIRFANSSG GDLEVTTHSF NCGGEFFYCN TSGLFNSTWI SNTSVQGSNS TGSNDSITLP CRIKQIINMW QRIGQAMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRRRAVGI GAVFLGFLGA AGSTMGAASM TLTVQARNLL SGIVQQQSNL LRAPEAQQHL LKLTVWGIKQ LQARVLAVER YLRDQQLLGI WGCSGKLICC TNVPWNSSWS NRNLSEIWDN MTWLQWDKEI SNYTQIIYGL LEESQNQQEK NEQDLLALD

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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 GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 200 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: 22000

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.99.67) / Number subtomograms used: 28262
ExtractionNumber tomograms: 69 / Number images used: 50329 / Software - Name: EMAN2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING

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