+Open data
-Basic information
Entry | Database: PDB / ID: 7asl | ||||||
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Title | HIV-1 Gag immature lattice. GagSP1T8I | ||||||
Components | Gag proteinHIV-1 protease | ||||||
Keywords | VIRAL PROTEIN / HIV / Gag / immature lattice / CA-SP1 / T8I | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Mendonca, L. / Zhang, P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Commun Biol / Year: 2021 Title: CryoET structures of immature HIV Gag reveal six-helix bundle. Authors: Luiza Mendonça / Dapeng Sun / Jiying Ning / Jiwei Liu / Abhay Kotecha / Mateusz Olek / Thomas Frosio / Xiaofeng Fu / Benjamin A Himes / Alex B Kleinpeter / Eric O Freed / Jing Zhou / ...Authors: Luiza Mendonça / Dapeng Sun / Jiying Ning / Jiwei Liu / Abhay Kotecha / Mateusz Olek / Thomas Frosio / Xiaofeng Fu / Benjamin A Himes / Alex B Kleinpeter / Eric O Freed / Jing Zhou / Christopher Aiken / Peijun Zhang / Abstract: Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), ...Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), SP2 and p6 domains. SP1, together with the last eight residues of CA, have been hypothesized to form a six-helix bundle responsible for the higher-order multimerization of Gag necessary for HIV particle assembly. However, the structure of the complete six-helix bundle has been elusive. Here, we determined the structures of both Gag in vitro assemblies and Gag viral-like particles (VLPs) to 4.2 Å and 4.5 Å resolutions using cryo-electron tomography and subtomogram averaging by emClarity. A single amino acid mutation (T8I) in SP1 stabilizes the six-helix bundle, allowing to discern the entire CA-SP1 helix connecting to the NC domain. These structures provide a blueprint for future development of small molecule inhibitors that can lock SP1 in a stable helical conformation, interfere with virus maturation, and thus block HIV-1 infection. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7asl.cif.gz | 680.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7asl.ent.gz | 589.3 KB | Display | PDB format |
PDBx/mmJSON format | 7asl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/7asl ftp://data.pdbj.org/pub/pdb/validation_reports/as/7asl | HTTPS FTP |
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-Related structure data
Related structure data | 11897MC 7ashC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 25944.766 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Homo sapiens (human) / Strain (production host): HEK293T / References: UniProt: C9DXR6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Human immunodeficiency virus 1Subtypes of HIV / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Source (recombinant) | Organism: Homo sapiens (human) / Strain: HEK293T |
Details of virus | Empty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.4 |
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: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 120 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_3699: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50343 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 46 / Num. of volumes extracted: 50343 | ||||||||||||||||||||||||
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