+Open data
-Basic information
Entry | Database: PDB / ID: 7urn | |||||||||
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Title | Structure of HIV-1 capsid declination | |||||||||
Components | HIV-1 capsid protein | |||||||||
Keywords | VIRUS LIKE PARTICLE / HIV-1 / capsid / declination / pentamer / hexamer | |||||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / 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 1 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å | |||||||||
Authors | Pornillos, O. / Ganser-Pornillos, B.K. / Schirra, R.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: A molecular switch modulates assembly and host factor binding of the HIV-1 capsid. Authors: Randall T Schirra / Nayara F B Dos Santos / Kaneil K Zadrozny / Iga Kucharska / Barbie K Ganser-Pornillos / Owen Pornillos / Abstract: The HIV-1 capsid is a fullerene cone made of quasi-equivalent hexamers and pentamers of the viral CA protein. Typically, quasi-equivalent assembly of viral capsid subunits is controlled by a ...The HIV-1 capsid is a fullerene cone made of quasi-equivalent hexamers and pentamers of the viral CA protein. Typically, quasi-equivalent assembly of viral capsid subunits is controlled by a molecular switch. Here, we identify a Thr-Val-Gly-Gly motif that modulates CA hexamer/pentamer switching by folding into a 3 helix in the pentamer and random coil in the hexamer. Manipulating the coil/helix configuration of the motif allowed us to control pentamer and hexamer formation in a predictable manner, thus proving its function as a molecular switch. Importantly, the switch also remodels the common binding site for host factors that are critical for viral replication and the new ultra-potent HIV-1 inhibitor lenacapavir. This study reveals that a critical assembly element also modulates the post-assembly and viral replication functions of the HIV-1 capsid and provides new insights on capsid function and inhibition. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7urn.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7urn.ent.gz | 212.3 KB | Display | PDB format |
PDBx/mmJSON format | 7urn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7urn_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7urn_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7urn_validation.xml.gz | 57.4 KB | Display | |
Data in CIF | 7urn_validation.cif.gz | 84.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/7urn ftp://data.pdbj.org/pub/pdb/validation_reports/ur/7urn | HTTPS FTP |
-Related structure data
Related structure data | 26715MC 7urtC 8eepC 8eetC 8ejlC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 25630.426 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: Gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493 #2: Chemical | Has ligand of interest | Y | |
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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: Capsid-like particles of in vitro assembled HIV-1 CA protein Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Manual plunge-freezing |
-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 defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 525219 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: The following protein chains were refined separately in real space using Phenix: A (pentamer); L, M and N (half-hexamer). Chain M was then rigid-body fit to generate chains O, P and Q to ...Details: The following protein chains were refined separately in real space using Phenix: A (pentamer); L, M and N (half-hexamer). Chain M was then rigid-body fit to generate chains O, P and Q to complete the hexamer. Chains O, P and Q are deposited as polyALA models. | ||||||||||||||||||||
Atomic model building | PDB-ID: 4XFX Accession code: 4XFX / Source name: PDB / Type: experimental model |