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Yorodumi- PDB-7sep: Cryo-EM Structure of the RT component of the HIV-1 Pol Polyprotein -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sep | ||||||||||||
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Title | Cryo-EM Structure of the RT component of the HIV-1 Pol Polyprotein | ||||||||||||
Components | Gag-Pol polyprotein | ||||||||||||
Keywords | VIRAL PROTEIN / HIV-1 / enzyme / TRANSFERASE / HYDROLASE | ||||||||||||
Function / homology | Function and homology information HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||||||||
Biological species | Human immunodeficiency virus type 1 BH10 | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Lyumkis, D. / Passos, D. / Arnold, E. / Harrison, J.J.E. | ||||||||||||
Funding support | 3items
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Citation | Journal: Sci Adv / Year: 2022 Title: Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation. Authors: Jerry Joe E K Harrison / Dario Oliveira Passos / Jessica F Bruhn / Joseph D Bauman / Lynda Tuberty / Jeffrey J DeStefano / Francesc Xavier Ruiz / Dmitry Lyumkis / Eddy Arnold / Abstract: Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields ...Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields the HIV structural proteins and enzymes. Structures of the mature enzymes PR, reverse transcriptase (RT), and integrase (IN) aided understanding of catalysis and design of antiretrovirals, but knowledge of the Pol precursor architecture and function before PR cleavage is limited. We developed a system to produce stable HIV-1 Pol and determined its cryo-electron microscopy structure. RT in Pol has a similar arrangement to the mature RT heterodimer, and its dimerization may draw together two PR monomers to activate proteolytic processing. HIV-1 thus may leverage the dimerization interfaces in Pol to regulate assembly and maturation of polyprotein precursors. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sep.cif.gz | 203.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sep.ent.gz | 144.8 KB | Display | PDB format |
PDBx/mmJSON format | 7sep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sep_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7sep_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7sep_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 7sep_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/7sep ftp://data.pdbj.org/pub/pdb/validation_reports/se/7sep | HTTPS FTP |
-Related structure data
Related structure data | 25074MC 7sjxC 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: 119289.867 Da / Num. of mol.: 2 / Fragment: PR-RT portion, residues 479-1447 / Mutation: D131A, L765D, F766D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03366 |
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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: RT portion of HIV-1 Pol / Type: COMPLEX Details: 3D reconstruction of the HIV-1 Pol polyprotein comprising the RT portion Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.12 MDa / Experimental value: NO |
Source (natural) | Organism: Human immunodeficiency virus type 1 BH10 |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.3 mg/ml / 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 / Cs: 2.7 mm |
Image recording | Electron dose: 0.95 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 60 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 27555 | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27555 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.11 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints |
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