+Open data
-Basic information
Entry | Database: PDB / ID: 8fzc | ||||||||||||||||||||||||
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Title | HIV-2 Gag Capsid from Immature Virus-like Particles | ||||||||||||||||||||||||
Components | Spacer peptide 2 | ||||||||||||||||||||||||
Keywords | VIRUS LIKE PARTICLE / Retrovirus / Lentivirus / Gag / Capsid / HIV-2 / lattice | ||||||||||||||||||||||||
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 | ||||||||||||||||||||||||
Biological species | Human immunodeficiency virus type 2 | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å | ||||||||||||||||||||||||
Authors | Talledge, N. / Zhang, W. / Mansky, L.M. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fzc.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fzc.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 8fzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fzc_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8fzc_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8fzc_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 8fzc_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/8fzc ftp://data.pdbj.org/pub/pdb/validation_reports/fz/8fzc | HTTPS FTP |
-Related structure data
Related structure data | 29607MC 7tv2C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 25109.822 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 2 (ISOLATE ROD) Gene: gag / Variant: isolate ROD / Plasmid: pN3 / Details (production host): CMV promotor / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P04590 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human immunodeficiency virus type 2 (ISOLATE ROD) / Type: VIRUS Details: HIV-2 VLPs generated by Gag co-overexpressed with HIV-2 Env in Hek293T cells and purified from media supernatant Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Human immunodeficiency virus type 2 (ISOLATE ROD) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||
Virus shell | Name: Capsid / Diameter: 2100 nm | ||||||||||||||||||||
Buffer solution | pH: 8 / Details: 100 mM NaCl, 10 mM Tris-HCL pH 8.0, 1mM EDTA | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: Leica ACE600 Glow Discharger. / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 292.15 K / Details: Leica GP2 Grid Plunger. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2250 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 10 / Num. of real images: 2508 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46017 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Chain-ID: A / Pdb chain-ID: A / Source name: PDB / Type: experimental model
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