+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11899 | |||||||||
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Title | HIV-1 Gag immature lattice. GagdeltaMASP1T8I with IP-6 | |||||||||
Map data | HIV-1 GagdeltaMASP1T8I with IP-6. | |||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Mendonca L / Zhang P | |||||||||
Funding support | United Kingdom, 1 items
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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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11899.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-11899-v30.xml emd-11899.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_11899.png | 83.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11899 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11899 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11899.map.gz / Format: CCP4 / Size: 69.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HIV-1 GagdeltaMASP1T8I with IP-6. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.196 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human immunodeficiency virus 1
Entire | Name: Human immunodeficiency virus 1 |
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Components |
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-Supramolecule #1: Human immunodeficiency virus 1
Supramolecule | Name: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Host system | Organism: Escherichia coli (E. coli) / Recombinant strain: Rosetta 2 DE3 |
Virus shell | Shell ID: 1 / Name: Gag |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 120.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 13 / Number images used: 29938 / Software - Name: emClarity |
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CTF correction | Software - Name: emClarity |
Final angle assignment | Type: OTHER / Software - Name: emClarity |
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 22822 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 94.38 / Target criteria: CC |