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- EMDB-25809: Sub-tomogram averaged map of HIV-Env with Gag layer from immature VLPs -

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Basic information

Entry
Database: EMDB / ID: EMD-25809
TitleSub-tomogram averaged map of HIV-Env with Gag layer from immature VLPs
Map dataImmature hVLP Env (relaxed C1 sym) with Gag layer - half map
Sample
  • Virus: Human immunodeficiency virus 1
KeywordsHIV-1 / envelope protein / glycoprotein / Env / membrane bound / VIRAL PROTEIN / Gag
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / stimulatory C-type lectin receptor signaling pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing ...virus-mediated perturbation of host defense response => GO:0019049 / : / stimulatory C-type lectin receptor signaling pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 Å
AuthorsMangala Prasad V / Lee KK
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI140868 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM099989 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143563 United States
CitationJournal: Cell / Year: 2022
Title: Cryo-ET of Env on intact HIV virions reveals structural variation and positioning on the Gag lattice.
Authors: Vidya Mangala Prasad / Daniel P Leaman / Klaus N Lovendahl / Jacob T Croft / Mark A Benhaim / Edgar A Hodge / Michael B Zwick / Kelly K Lee /
Abstract: HIV-1 Env mediates viral entry into host cells and is the sole target for neutralizing antibodies. However, Env structure and organization in its native virion context has eluded detailed ...HIV-1 Env mediates viral entry into host cells and is the sole target for neutralizing antibodies. However, Env structure and organization in its native virion context has eluded detailed characterization. Here, we used cryo-electron tomography to analyze Env in mature and immature HIV-1 particles. Immature particles showed distinct Env positioning relative to the underlying Gag lattice, providing insights into long-standing questions about Env incorporation. A 9.1-Å sub-tomogram-averaged reconstruction of virion-bound Env in conjunction with structural mass spectrometry revealed unexpected features, including a variable central core of the gp41 subunit, heterogeneous glycosylation between protomers, and a flexible stalk that allows Env tilting and variable exposure of neutralizing epitopes. Together, our results provide an integrative understanding of HIV assembly and structural variation in Env antigen presentation.
History
DepositionDec 23, 2021-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25809.png

Downloads & links

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Map

FileDownload / File: emd_25809.map.gz / Format: CCP4 / Size: 128.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImmature hVLP Env (relaxed C1 sym) with Gag layer - half map
Voxel sizeX=Y=Z: 10.32 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-6.102888 - 7.1097636
Average (Standard dev.)0.000000004897728 (±0.99998474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-16-16-16
Dimensions323232
Spacing323232
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.3210.3210.32
M x/y/z323232
origin x/y/z0.0000.0000.000
length x/y/z330.240330.240330.240
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS-16-16-16
NC/NR/NS323232
D min/max/mean-6.1037.1100.000

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Supplemental data

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Additional map: Immature hVLP Env (relaxed C1 sym) with Gag layer - full combined map

Fileemd_25809_additional_1.map
AnnotationImmature hVLP Env (relaxed C1 sym) with Gag layer - full combined 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 / Macromolecule list: #1
Details: HIV-1 ADA.CM Env glycoprotein displayed on high Env expressing VLPs
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / Strain: ADA.CM
Molecular weightTheoretical: 400 KDa
Virus shellShell ID: 1 / Name: Outer membrane envelope / Diameter: 1000.0 Å

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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 / Component - Concentration: 1.0 X / Component - Name: Phosphate buffer saline / Details: 1X PBS at pH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3ul sample, blotting time of 4-5 seconds.
DetailsImmature VLP particles displaying nearly full-length Env glycoprotein on membrane surface

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 58000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 34.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 1520
ExtractionNumber tomograms: 20 / Number images used: 1520 / Method: Volumes picked semi-automatically / Software - Name: PEET / Details: Using semi-automated picking in PEET software
Final 3D classificationSoftware - Name: EMAN2
Final angle assignmentType: OTHER / Software - Name: EMAN2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ska


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailshVLP-Env on membrane surface
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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Atomic model buiding 2

Initial modelPDB ID:

4usn


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsGag-CA hexamer structure for inner protein layer under membrane bilayer
RefinementProtocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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