CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.
Meghna GuptaCaleigh M AzumayaMichelle MoritzSergei PourmalAmy DialloGregory E MerzGwendolyn M JangMehdi BouhaddouAndrea FossatiAxel F BrilotDevan DiwanjiEvelyn HernandezNadia HerreraHuong T KratochvilVictor L LamFei LiYang LiHenry C NguyenCarlos A NowotnyTristan W OwensJessica K PetersAlexandrea N RizoUrsula Schulze-GahmenAmber M SmithIris D YoungZanlin YuDaniel E AsarnowChristian B BillesbølleMelody G CampbellJen ChenKuei-Ho ChenUn Seng ChioMiles Sasha DickinsonLoan DoanMingliang JinSun Kyung KimJunrui LiGrant J JensenEdmond M LinossiYanxin LiuMegan LoJocelyne LopezKyle E LopezAdamo S MancinoFrank R MossMichael D PaulKomal Ishwar PawarAdrian PelinThomas H PospiechCristina PuchadesSoumya Govinda RemeshMaliheh SafariKaitlin SchaeferMing SunMariano C TabiosAye C ThwinErron W TitusRaphael TrenkerEric TseTsz Kin Martin TsuiFeng WangKaihua ZhangSunny ZhangJianhua ZhaoFengbo ZhouYuan ZhouLorena Zuliani-Alvareznull nullDavid A AgardYifan ChengBrian K ShoichetNatalia JuraTanja KortemmeAashish ManglikDaniel R SouthworthRobert M StroudDanielle L SwaneyNevan J KroganAdam FrostOren S RosenbergKliment A VerbaPublished in: bioRxiv : the preprint server for biology (2021)
The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.
Keyphrases
- sars cov
- respiratory syndrome coronavirus
- electron microscopy
- high resolution
- mass spectrometry
- quality control
- transcription factor
- deep learning
- protein protein
- binding protein
- amino acid
- structural basis
- small molecule
- genome wide
- artificial intelligence
- drug delivery
- emergency department
- gene expression
- dna methylation
- single cell
- high density
- liquid chromatography
- ms ms
- high performance liquid chromatography
- cell migration