+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29777 | ||||||||||||||||||
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Title | Defective HIV-1 CA pentamer in surrounding hexameric lattice | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | ||||||||||||||||||
Authors | Highland CM / Dick RA | ||||||||||||||||||
Funding support | United States, United Kingdom, 5 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structural insights into HIV-1 polyanion-dependent capsid lattice formation revealed by single particle cryo-EM. Authors: Carolyn M Highland / Aaron Tan / Clifton L Ricaña / John A G Briggs / Robert A Dick / Abstract: The HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical ...The HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical fullerene lattice composed of roughly 200 CA hexamers and 12 CA pentamers. Previous structural analyses of individual CA hexamers and pentamers have provided valuable insight into capsid structure and function, but detailed structural information about these assemblies in the broader context of the capsid lattice is lacking. In this study, we combined cryoelectron tomography and single particle analysis (SPA) cryoelectron microscopy to determine structures of continuous regions of the capsid lattice containing both hexamers and pentamers. We also developed a method of liposome scaffold-based in vitro lattice assembly ("lattice templating") that enabled us to directly study the lattice under a wider range of conditions than has previously been possible. Using this approach, we identified a critical role for inositol hexakisphosphate in pentamer formation and determined the structure of the CA lattice bound to the capsid-targeting antiretroviral drug GS-6207 (lenacapavir). Our work reveals key structural details of the mature HIV-1 CA lattice and establishes the combination of lattice templating and SPA as a robust strategy for studying retroviral capsid structure and capsid interactions with host proteins and antiviral compounds. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29777.map.gz | 138.8 MB | EMDB map data format | |
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Header (meta data) | emd-29777-v30.xml emd-29777.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_29777.png | 65.2 KB | ||
Masks | emd_29777_msk_1.map | 178 MB | Mask map | |
Others | emd_29777_half_map_1.map.gz emd_29777_half_map_2.map.gz | 140.2 MB 140.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29777 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29777 | HTTPS FTP |
-Validation report
Summary document | emd_29777_validation.pdf.gz | 989.7 KB | Display | EMDB validaton report |
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Full document | emd_29777_full_validation.pdf.gz | 989.3 KB | Display | |
Data in XML | emd_29777_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_29777_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29777 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29777 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29777.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29777_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29777_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29777_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Defective HIV-1 capsid (CA) pentamer within surrounding hexameric...
Entire | Name: Defective HIV-1 capsid (CA) pentamer within surrounding hexameric CA lattice |
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Components |
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-Supramolecule #1: Defective HIV-1 capsid (CA) pentamer within surrounding hexameric...
Supramolecule | Name: Defective HIV-1 capsid (CA) pentamer within surrounding hexameric CA lattice type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all Details: Partial HIV-1 capsid (CA) lattice assembled on small unilamellar vesicles at pH 7.4 in the absence of polyanionic assembly cofactor |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Sequence | String: MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE PFRDYVDRFY ...String: MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE PFRDYVDRFY KTLRAEQASQ EVKNWMTETL LVQNANPDCK TILKALGPGA TLEEMMTACQ GVGGPGHKAR VLHHHHHH |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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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: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11558 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |