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- EMDB-29607: HIV-2 Gag Capsid from Immature Virus-like Particles -

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Basic information

Entry
Database: EMDB / ID: EMD-29607
TitleHIV-2 Gag Capsid from Immature Virus-like Particles
Map dataPostprocessed masked map.
Sample
  • Virus: Human immunodeficiency virus type 2 (ISOLATE ROD)
    • Protein or peptide: Spacer peptide 2
KeywordsRetrovirus / Lentivirus / Gag / Capsid / HIV-2 / lattice / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 2 (ISOLATE ROD)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsTalledge N / Zhang W / Mansky LM
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) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29607.png

Downloads & links

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Map

FileDownload / File: emd_29607.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed masked map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.031590365 - 0.03839835
Average (Standard dev.)0.000089975045 (±0.0012553501)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29607_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed unmasked map.

Fileemd_29607_additional_1.map
AnnotationPostprocessed unmasked map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map even set.

Fileemd_29607_half_map_1.map
AnnotationHalf map even set.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map odd set.

Fileemd_29607_half_map_2.map
AnnotationHalf map odd set.
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: Spacer peptide 2

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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: Spacer peptide 2

MacromoleculeName: Spacer peptide 2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus type 2 (ISOLATE ROD)
Molecular weightTheoretical: 25.109822 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPRTLNAWVK LVEEKKFGAE VVPGFQALSE GCTPYDINQM LNCVGDHQAA MQIIREIINE EAAEWDVQHP IPGPLPAGQL REPRGSDIA GTTSTVEEQI QWMFRPQNPV PVGNIYRRWI QIGLQKCVRM YNPTNILDIK QGPKEPFQSY VDRFYKSLRA E QTDPAVKN ...String:
SPRTLNAWVK LVEEKKFGAE VVPGFQALSE GCTPYDINQM LNCVGDHQAA MQIIREIINE EAAEWDVQHP IPGPLPAGQL REPRGSDIA GTTSTVEEQI QWMFRPQNPV PVGNIYRRWI QIGLQKCVRM YNPTNILDIK QGPKEPFQSY VDRFYKSLRA E QTDPAVKN WMTQTLLVQN ANPDCKLVLK GLGMNPTLEE MLTACQGVGG PGQKARLMAE ALKEVI

UniProtKB: Gag polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
10.0 mMC4H11NO3Tris-HCl
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 / Details: Leica ACE600 Glow Discharger.
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 292.15 K / Instrument: LEICA EM GP / Details: Leica GP2 Grid Plunger..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 10 / Number real images: 2508 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
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

Startup modelType of model: EMDB MAP
EMDB ID:

4015


Details: Low pass filtered to 60 Angstroms.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 46017
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 43864 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

2wlv

chain_id: A, source_name: PDB, initial_model_type: experimental model

5l93

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8fzc:
HIV-2 Gag Capsid from Immature Virus-like Particles

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