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TitleOligomeric HIV-1 integrase structures reveal functional plasticity for intasome assembly and RNA binding.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 9430, Year 2025
Publish dateOct 24, 2025
AuthorsTao Jing / Zelin Shan / Tung Dinh / Avik Biswas / Sooin Jang / Juliet Greenwood / Min Li / Zeyuan Zhang / Gennavieve Gray / Hye Jeong Shin / Bo Zhou / Dario Passos / Timothy S Strutzenberg / Sriram Aiyer / Leonardo Andrade / Yuxuan Zhang / Zhen Li / Robert Craigie / Alan N Engelman / Mamuka Kvaratskhelia / Dmitry Lyumkis /
PubMed AbstractIntegrase (IN) performs dual essential roles during HIV-1 replication. During ingress, IN functions within an oligomeric "intasome" assembly to catalyze viral DNA integration into host chromatin. ...Integrase (IN) performs dual essential roles during HIV-1 replication. During ingress, IN functions within an oligomeric "intasome" assembly to catalyze viral DNA integration into host chromatin. During late stages of infection, tetrameric IN binds viral RNA and orchestrates the condensation of ribonucleoprotein complexes into the capsid core. The molecular architectures of HIV-1 IN assemblies that mediate these distinct events remain unknown. Furthermore, the IN tetramer is an important antiviral target for investigational allosteric IN inhibitors. Here, we determined cryo-EM structures of wildtype HIV-1 IN tetramers and intasome hexadecamers. Our structures unveil a remarkable plasticity that leverages IN C-terminal domains and abutting linkers to assemble functionally distinct oligomeric forms. Alteration of a newly recognized conserved interface revealed that both IN functions track with tetramerization in vitro and during HIV-1 infection. Collectively, our findings reveal how IN plasticity orchestrates its diverse molecular functions and suggest a working model for IN-viral RNA binding. Moreover, our structure of the IN tetramer provides atomic blueprints for the rational development of improved allosteric inhibitors.
External linksNat Commun / PubMed:41136407 / PubMed Central
MethodsEM (single particle)
Resolution4.0 - 8.0 Å
Structure data

44962

9bw9

EMDB-44962, PDB-9bw9:
Tetrameric Complex of full-length HIV-1 integrase protein bound to the integrase binding domain of LEDGF/p75
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-45103: Consensus map of NL4-3 WT HIV-1 intasome
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-45104: Top half of NL4-3 WT HIV-1 intasome
Method: EM (single particle) / Resolution: 5.0 Å

EMDB-45150: Bottom half of NL4-3 WT HIV-1 intasome
Method: EM (single particle) / Resolution: 5.3 Å

45151

9c29

EMDB-45151, PDB-9c29:
Hexadecamer of NL4-3 WT HIV-1 intasome
Method: EM (single particle) / Resolution: 8.0 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • HIV type 1 (virus)
  • homo sapiens (human)
  • hiv-1 06tg.ht008 (virus)
KeywordsVIRAL PROTEIN / protein complex / hydrolase / VIRAL PROTEIN/DNA / VIRAL PROTEIN-DNA complex

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