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- EMDB-74779: HIV-1 CH505.N197D Env Ectodomain (Immature VLPs) -

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Basic information

Entry
Database: EMDB / ID: EMD-74779
TitleHIV-1 CH505.N197D Env Ectodomain (Immature VLPs)
Map dataHIV-1 CH505.N197D Env Ectodomain (Immature VLPs)
Sample
  • Virus: HIV-1 06TG.HT008 (virus)
    • Protein or peptide: CH505.N197D Envelope Protein
KeywordsHIV-1 / Env / membrane / fusion / VIRAL PROTEIN
Biological speciesHIV-1 06TG.HT008 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 8.9 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_74779.png

Downloads & links

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Map

FileDownload / File: emd_74779.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 CH505.N197D Env Ectodomain (Immature VLPs)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.72 Å/pix.
x 96 pix.
= 357.12 Å		3.72 Å/pix.
x 96 pix.
= 357.12 Å		3.72 Å/pix.
x 96 pix.
= 357.12 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: 2.49
Minimum - Maximum-19.442170999999998 - 23.30555
Average (Standard dev.)0.019445363 (±0.9244086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions969696
Spacing969696
CellA=B=C: 357.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HIV-1 CH505.N197D Env Ectodomain (Immature VLPs) half map 1

Fileemd_74779_half_map_1.map
AnnotationHIV-1 CH505.N197D Env Ectodomain (Immature VLPs) half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 CH505.N197D Env Ectodomain (Immature VLPs) half map 2

Fileemd_74779_half_map_2.map
AnnotationHIV-1 CH505.N197D Env Ectodomain (Immature VLPs) 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: CH505.N197D Envelope Protein

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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: CH505.N197D Envelope Protein

MacromoleculeName: CH505.N197D Envelope Protein / type: protein_or_peptide / ID: 1
Details: CH505.N197D Envelope Protein (HIV-1, immature VLPs)
Enantiomer: LEVO
Source (natural)Organism: HIV-1 06TG.HT008 (virus) / Strain: CH505.N197D
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGMWV TVYYGVPVWK EAKTTLFCAS DAKAYEKEVH NVWATHACVP TDPNPQEMVL KNVTENFNMW KNDMVDQMHE DVISLWDQSL KPCVKLTPLC VTLNCTNATA SNSSIIEGMK NCSFNITTEL RDKREKKNAL ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGMWV TVYYGVPVWK EAKTTLFCAS DAKAYEKEVH NVWATHACVP TDPNPQEMVL KNVTENFNMW KNDMVDQMHE DVISLWDQSL KPCVKLTPLC VTLNCTNATA SNSSIIEGMK NCSFNITTEL RDKREKKNAL FYKLDIVQLD GNSSQYRLIN CDTSVITQAC PKVSFDPIPI HYCAPAGYAI LKCNNKTFTG TGPCNNVSTV QCTHGIKPVV STQLLLNGSL AEGEIIIRSE NITNNVKTII VHLNESVKIE CTRPNNKTRT SIRIGPGQAF YATGQVIGDI REAYCNINES KWNETLQRVS KKLKEYFPHK NITFQPSSGG DLEITTHSFN CGGEFFYCNT SSLFNRTYMA NSTDMANSTE TNSTRTITIH CRIKQIINMW QEVGRAMYAP PIAGNITCIS NITGLLLTRD GGKNNTETFR PGGGNMKDNW RSELYKYKVV EVKPLGVAPT NARRRVVERR RRRRAVGMGA VFLGFLGAAG STMGAASITL TVQARQLLSG IVQQQSNLLK AIEAQQHMLK LTVWGIKQLQ ARVLALERYL KDQQLLGMWG CSGKLICTTN VYWNSSWSNK TYGDIWDNMT WMQWEREISN YTEIIYELLE ESQNQQEKNE QDLLALDRWN SLWNWFNITN WLWYIKIFIM IVGGLIGLRI IFAVLSLVNR VRQGYSPLSL QTLIPSPRGP DRPGGIEEEG GEQDRNRSTR LVSGFLALVW DDLRSLCLFI YHRLRDFILI AARAGELLGR SSLKGLRRGW EALKYLGSLV QYWGLELKRS AISLLDTLAI AVGEGTDRIL EFVLGICRAI RNIPTRIRQG FETALL

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.99.67) / Number subtomograms used: 3797
ExtractionNumber tomograms: 233 / Number images used: 20719 / Method: Manual / Software - Name: EMAN2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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