+Open data
-Basic information
Entry | Database: PDB / ID: 8ty6 | ||||||
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Title | Disulfide-stabilized HIV-1 CA hexamer in complex with PQBP1 Nt | ||||||
Components | Capsid protein p24 | ||||||
Keywords | VIRAL PROTEIN / capsid / innate immune sensor | ||||||
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 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Piacentini, J. / Pornillos, O. / Ganser-Pornillos, B.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Mol Biol / Year: 2024 Title: Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice. Authors: Juliana Piacentini / Dale S Allen / Barbie K Ganser-Pornillos / Sumit K Chanda / Sunnie M Yoh / Owen Pornillos / Abstract: Human immunodeficiency virus type 1 (HIV-1) stimulates innate immune responses upon infection, including cyclic GMP-AMP synthase (cGAS) signaling that results in type I interferon production. HIV-1- ...Human immunodeficiency virus type 1 (HIV-1) stimulates innate immune responses upon infection, including cyclic GMP-AMP synthase (cGAS) signaling that results in type I interferon production. HIV-1-induced activation of cGAS requires the host cell factor polyglutamine binding protein 1 (PQBP1), an intrinsically disordered protein that bridges capsid recognition and cGAS recruitment. However, the molecular details of PQBP1 interactions with the HIV-1 capsid and their functional implications remain poorly understood. Here, we show that PQBP1 binds to HIV-1 capsids through charge complementing contacts between acidic residues in the N-terminal region of PQBP1 and an arginine ring in the central channel of the HIV-1 CA hexamer that makes up the viral capsid. These studies reveal the molecular details of PQBP1's primary interaction with the HIV-1 capsid and suggest that additional elements are likely to contribute to stable capsid binding. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ty6.cif.gz | 241.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ty6.ent.gz | 196.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ty6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ty6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ty6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ty6_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 8ty6_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/8ty6 ftp://data.pdbj.org/pub/pdb/validation_reports/ty/8ty6 | HTTPS FTP |
-Related structure data
Related structure data | 41711MC 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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1 |
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-Components
#1: Protein | Mass: 25461.271 Da / Num. of mol.: 6 / Mutation: A14C, E45C, W184A, M185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493 |
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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: HIV-1 CA hexamer bound to PQBP1 Nt peptide / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Human immunodeficiency virus 1 |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 312788 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 3H47 Accession code: 3H47 / Details: 3H47 chain A docked into map / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
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