+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29606 | ||||||||||||||||||||||||
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Title | CryoET of HIV-2 Immature Particles | ||||||||||||||||||||||||
Map data | Odd half map | ||||||||||||||||||||||||
Sample |
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Keywords | Retrovirus / Lentivirus / Gag / Capsid / HIV-2 / lattice / VIRUS LIKE PARTICLE | ||||||||||||||||||||||||
Biological species | Human immunodeficiency virus 2 / Human immunodeficiency virus type 2 (ISOLATE ROD) | ||||||||||||||||||||||||
Method | electron tomography / cryo EM / Resolution: 9.1 Å | ||||||||||||||||||||||||
Authors | Talledge N / Zhang W / Mansky ML | ||||||||||||||||||||||||
Funding support | United States, 7 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29606.map.gz | 29.1 MB | EMDB map data format | |
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Header (meta data) | emd-29606-v30.xml emd-29606.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29606_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_29606.png | 59.8 KB | ||
Masks | emd_29606_msk_1.map | 64 MB | Mask map | |
Others | emd_29606_half_map_1.map.gz emd_29606_half_map_2.map.gz | 48.8 MB 48.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29606 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29606 | HTTPS FTP |
-Validation report
Summary document | emd_29606_validation.pdf.gz | 441.2 KB | Display | EMDB validaton report |
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Full document | emd_29606_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | emd_29606_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_29606_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29606 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29606 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29606.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Annotation | Odd half map | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29606_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Even half map
File | emd_29606_half_map_1.map | ||||||||||||
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Annotation | Even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Odd half map
File | emd_29606_half_map_2.map | ||||||||||||
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Annotation | Odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human immunodeficiency virus type 2 (ISOLATE ROD)
Entire | Name: Human immunodeficiency virus type 2 (ISOLATE ROD) |
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Components |
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-Supramolecule #1: Human immunodeficiency virus type 2 (ISOLATE ROD)
Supramolecule | Name: 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 |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 2100.0 Å |
-Macromolecule #1: HIV-2 Immature Gag
Macromolecule | Name: HIV-2 Immature Gag / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 2 / Strain: Rod |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: 100 mM NaCl, 10 mM Tris-HCL pH 8.0, 1mM EDTA | ||||||||||||
Grid | Model: 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 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 292.15 K / Instrument: LEICA EM GP / Details: Leica GP2 Grid Plunger.. | ||||||||||||
Sectioning | Other: NO SECTIONING | ||||||||||||
Fiducial marker | Manufacturer: Ted pella / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |