Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G

Hanjing Yang, Kyumin Kim, Shuxing Li, Josue Pacheco and Xiaojiang S. Chen ()
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Hanjing Yang: Molecular and Computational Biology, Departments of Biological Sciences and Chemistry
Kyumin Kim: Molecular and Computational Biology, Departments of Biological Sciences and Chemistry
Shuxing Li: Molecular and Computational Biology, Departments of Biological Sciences and Chemistry
Josue Pacheco: Molecular and Computational Biology, Departments of Biological Sciences and Chemistry
Xiaojiang S. Chen: Molecular and Computational Biology, Departments of Biological Sciences and Chemistry

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract An essential step in restricting HIV infectivity by the antiviral factor APOBEC3G is its incorporation into progeny virions via binding to HIV RNA. However, the mechanism of APOBEC3G capturing viral RNA is unknown. Here, we report crystal structures of a primate APOBEC3G bound to different types of RNAs, revealing that APOBEC3G specifically recognizes unpaired 5’-AA-3’ dinucleotides, and to a lesser extent, 5’-GA-3’ dinucleotides. APOBEC3G binds to the common 3’A in the AA/GA motifs using an aromatic/hydrophobic pocket in the non-catalytic domain. It binds to the 5’A or 5’G in the AA/GA motifs using an aromatic/hydrophobic groove conformed between the non-catalytic and catalytic domains. APOBEC3G RNA binding property is distinct from that of the HIV nucleocapsid protein recognizing unpaired guanosines. Our findings suggest that the sequence-specific RNA recognition is critical for APOBEC3G virion packaging and restricting HIV infectivity.

Date: 2022
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DOI: 10.1038/s41467-022-35201-9

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