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- EMDB-29606: CryoET of HIV-2 Immature Particles -

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Basic information

Entry
Database: EMDB / ID: EMD-29606
TitleCryoET of HIV-2 Immature Particles
Map dataOdd half map
Sample
  • Virus: Human immunodeficiency virus type 2 (ISOLATE ROD)
    • Protein or peptide: HIV-2 Immature Gag
KeywordsRetrovirus / Lentivirus / Gag / Capsid / HIV-2 / lattice / VIRUS LIKE PARTICLE
Biological speciesHuman immunodeficiency virus 2 / Human immunodeficiency virus type 2 (ISOLATE ROD)
Methodelectron tomography / cryo EM / Resolution: 9.1 Å
AuthorsTalledge N / Zhang W / Mansky ML
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)124279 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118047 United States
National Science Foundation (NSF, United States)DMR-2011401 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)124165 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)007097 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)150351 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)83196 United States
CitationJournal: J Mol Biol / Year: 2023
Title: HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation.
Authors: Nathaniel Talledge / Huixin Yang / Ke Shi / Raffaele Coray / Guichuan Yu / William G Arndt / Shuyu Meng / Gloria C Baxter / Luiza M Mendonça / Daniel Castaño-Díez / Hideki Aihara / Louis ...Authors: Nathaniel Talledge / Huixin Yang / Ke Shi / Raffaele Coray / Guichuan Yu / William G Arndt / Shuyu Meng / Gloria C Baxter / Luiza M Mendonça / Daniel Castaño-Díez / Hideki Aihara / Louis M Mansky / Wei Zhang /
Abstract: Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus ...Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10-12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.
History
DepositionJan 28, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29606.png

Downloads & links

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Map

FileDownload / File: emd_29606.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOdd half map
Voxel sizeX=Y=Z: 1.32 Å
Density
Minimum - Maximum-0.008679926 - 0.016046163
Average (Standard dev.)0.00026240936 (±0.0009815186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29606_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Even half map

Fileemd_29606_half_map_1.map
AnnotationEven half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Odd half map

Fileemd_29606_half_map_2.map
AnnotationOdd half 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 type 2 (ISOLATE ROD)

EntireName: Human immunodeficiency virus type 2 (ISOLATE ROD)
Components
  • Virus: Human immunodeficiency virus type 2 (ISOLATE ROD)
    • Protein or peptide: HIV-2 Immature Gag

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Supramolecule #1: Human immunodeficiency virus type 2 (ISOLATE ROD)

SupramoleculeName: Human immunodeficiency virus type 2 (ISOLATE ROD) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: HIV-2 VLPs generated by Gag co-overexpressed with HIV-2 Env in Hek293T cells and purified from media supernatant
NCBI-ID: 11720
Sci species name: Human immunodeficiency virus type 2 (ISOLATE ROD)
Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 2100.0 Å

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Macromolecule #1: HIV-2 Immature Gag

MacromoleculeName: HIV-2 Immature Gag / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: Rod
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGARNSVLRG KKADELERIR LRPGGKKKYR LKHIVWAANK LDRFGLAESL LESKEGCQKI LTVLDPMVP TGSENLKSLF NTVCVIWCIH AEEKVKDTEG AKQIVRRHLV AETGTAEKMP S TSRPTAPS SEKGGNYPVQ HVGGNYTHIP LSPRTLNAWV KLVEEKKFGA ...String:
MGARNSVLRG KKADELERIR LRPGGKKKYR LKHIVWAANK LDRFGLAESL LESKEGCQKI LTVLDPMVP TGSENLKSLF NTVCVIWCIH AEEKVKDTEG AKQIVRRHLV AETGTAEKMP S TSRPTAPS SEKGGNYPVQ HVGGNYTHIP LSPRTLNAWV KLVEEKKFGA EVVPGFQALS EG CTPYDIN QMLNCVGDHQ AAMQIIREII NEEAAEWDVQ HPIPGPLPAG QLREPRGSDI AGT TSTVEE QIQWMFRPQN PVPVGNIYRR WIQIGLQKCV RMYNPTNILD IKQGPKEPFQ SYVD RFYKS LRAEQTDPAV KNWMTQTLLV QNANPDCKLV LKGLGMNPTL EEMLTACQGV GGPGQ KARL MAEALKEVIG PAPIPFAAAQ QRKAFKCWNC GKEGHSARQC RAPRRQGCWK CGKPGH IMT NCPDRQAGFL GLGPWGKKPR NFPVAQVPQG LTPTAPPVDP AVDLLEKYMQ QGKRQRE QR ERPYKEVTED LLHLEQGETP YREPPTEDLL HLNSLFGKDQ

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloridesodium chloride
10.0 mMC4H11NO3Tris-HClTris
1.0 mMC10H16N2O8Ethylenediaminetetraacetic acid

Details: 100 mM NaCl, 10 mM Tris-HCL pH 8.0, 1mM EDTA
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.001 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 292.15 K / Instrument: LEICA EM GP / Details: Leica GP2 Grid Plunger..
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Ted pella / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-8 / Number grids imaged: 2 / Number real images: 63 / Average exposure time: 2.0 sec. / Average electron dose: 1.1 e/Å2
Details: Two second exposures with a 0.25 frames/sec rate per tilt with a 1.1 e-/Angstrom^2 dose per tilt with a total tilt series dose of 45 e-/Angstroms^2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 13378
FSC plot (resolution estimation)

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