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Yorodumi- EMDB-46631: Gag CA-SP1 immature lattice from enveloped and perforated virus l... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-46631 | |||||||||
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Title | Gag CA-SP1 immature lattice from enveloped and perforated virus like particles | |||||||||
Map data | ||||||||||
Sample |
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Keywords | HIV-1 / Gag / CA-SP1 / Inhibitor / virion assembly / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Wu C / Meuser ME / Xiong Y | |||||||||
Funding support | United States, 2 items
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Citation | Journal: bioRxiv / Year: 2024 Title: Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution single-particle cryo-EM. Authors: Chunxiang Wu / Megan E Meuser / Juan S Rey / Hamed Meshkin / Rachel Yang / Swapnil Chandrakant Devarkar / Christian Freniere / Jiong Shi / Christopher Aiken / Juan R Perilla / Yong Xiong / Abstract: HIV-1 inhibitors, such as Bevirimat (BVM) and Lenacapavir (LEN), block the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence of high- ...HIV-1 inhibitors, such as Bevirimat (BVM) and Lenacapavir (LEN), block the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence of high-resolution structures for BVM complexes and LEN's structural data being limited to the mature capsid. Utilizing perforated virus-like particles (VLPs) produced from mammalian cells, we developed an approach to determine cryo-electron microscopy (cryo-EM) structures of HIV-1 with inhibitors. This allowed for the first structural determination of the native immature HIV-1 particle with BVM and LEN bound inside the VLPs at high resolutions. Our findings offer a more accurate model of BVM engaging the Gag lattice and, importantly, demonstrate that LEN not only binds the mature capsid but also targets the immature lattice in a distinct manner. The binding of LEN induces a conformational change in the capsid protein (CA) region and alters the architecture of the Gag lattice, which may affect the maturation process. These insights expand our understanding of the inhibitory mechanisms of BVM and LEN on HIV-1 and provide valuable clues for the design of future inhibitors. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_46631.map.gz | 75 MB | EMDB map data format | |
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Header (meta data) | emd-46631-v30.xml emd-46631.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_46631_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_46631.png | 207.9 KB | ||
Masks | emd_46631_msk_1.map | 158 MB | Mask map | |
Filedesc metadata | emd-46631.cif.gz | 6.5 KB | ||
Others | emd_46631_additional_1.map.gz emd_46631_half_map_1.map.gz emd_46631_half_map_2.map.gz | 147.1 MB 146 MB 146 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-46631 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-46631 | HTTPS FTP |
-Validation report
Summary document | emd_46631_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_46631_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_46631_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | emd_46631_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-46631 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-46631 | HTTPS FTP |
-Related structure data
Related structure data | 9d88MC 9cwvC 9d6cC 9d6dC 9d6eC 9dwdC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_46631.map.gz / Format: CCP4 / Size: 158 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.868 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_46631_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_46631_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_46631_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_46631_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Entire | Name: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) |
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Components |
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-Supramolecule #1: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Supramolecule | Name: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: NL-MA/NC DNA was transfected into Expi293F (ThermoTisher) cells and cultured in suspension culture. The enveloped virion like particles were purified by filtration and ultracentrifugation, ...Details: NL-MA/NC DNA was transfected into Expi293F (ThermoTisher) cells and cultured in suspension culture. The enveloped virion like particles were purified by filtration and ultracentrifugation, and directly used as cryo-EM sample. NCBI-ID: 11698 Sci species name: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) Sci species strain: Clone pNL4-3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Name: Gag |
-Macromolecule #1: Gag polyprotein
Macromolecule | Name: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) Strain: Clone pNL4-3 |
Molecular weight | Theoretical: 25.339037 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE PFRDYVDRFY K TLRAEQAS ...String: VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE PFRDYVDRFY K TLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGVGGPGHKA RVIAEAMSQV T UniProtKB: Gag polyprotein |
-Macromolecule #2: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: This is the final buffer in which the enveloped viral-like particle was resuspended. The Gag-CA-SP1 lattice is inside the virus-like particle and not directly in the buffer environment. | ||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III | ||||||||||||
Details | NL-MA/NC DNA was transfected into Expi293F (thermofisher) cells and cultured in suspension culture. The enveloped virion like particles were purified by filtration and ultracentrifugation, and directly used as cryo-EM sample. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |