Cell Symposia S3 Notes

SARS-Cov2 RNA capping

Zihe Rao, Tsinghua University

decoration of cap in viral RNA

Mechanisms for viral RNA capping: 3 pathways

VSV: use the second pathway COVID-19: use the first pathway

unique features of RdRp: N-terminal NiRAN domain

Nsp9, a single-strand RNA binding protein, joins to form an extend RTC

NiRAN is the GTase to form GpppA

NiRAN does not modify nsp9 at this moment

Nsp12 catalyzes a RNA modification on nsp9, RNAylation?

An essential ‘breaking-bond water’

A novel mechanism for RNA capping pathway

NAI-nsp9 inhibits RNAylation

AI-assisted drug design, AI-assisted NiRAN inhibitor design, calculate packing densities in NiRAN pockets

summary

• Identify the structure of polymerase NiRAN
• Discover the function of NiRAN in the conventional capping pathway
• Reveal a novel nsp9-RNAylation-mediated capping pathway catalyzed by NiRAN
• Rise a ‘induce-and-lock’ mechanism for inhibitor design targeting NiRAN against capping

in situ Structure Biology of Virus Infection

Peijun Zhang, University of Oxford, UK

HIV-1 life cycle: IP6, CypA, CPSF6, Nup358, BICD2, etc. host factors

HIV-1 maturation: HIV Gag protein

Gag assemblies, T8I mutant

T8I stabilizes the full 6HB, immature particles

small molecule in the immature core, in HEK-293 it is IP6

Mature capsid assembly, Mature capsomer is intrinsically curved

Host factor IP6 binding to the mature capsid

MD silumations of IP6 binding

Virus factory, cryo-FIB milling, cryo-ET, SLP, DLP

New opportunities for genomic organization and process

New cryoEM methods for studying native biological complexes, in situ and in action

Z. Hong Zhou, UCLA, USA

Isonet

Blue-tongue virus(BTV) assembly in cytoplasm

BTV assembly intermediates at high resolution

CryoID

Protozoa and Human diseases

Native complexes involved in pathogen trasmission

assembly of ankyrin complex

cryoEM and 2D class averages of cellular milieu

cryoID indentified

summary

• AI-based program IsoNet to recover missing-wedge for molecular sociology interpretation of cellular tomography
• cryoID for identification and modelling of native macromolecular complex structures in cellular milieu(protist infection)
  • Atomic structure of native protein complex SGS1 in mosquito salivary glands
  • Structures of nine complexes related to the ankyrin complex of red blood cell cytoskeleton
  • Novel RhopH complex involved in malaria nutrient uptake
  • Trapanosoma brucei: MCC, PCC and RNA-editing substrate-binding complex in multiple functional states

Protein quality control systems

AMBRA1, the activating molecule in Beclin-1-regulated autophagy

AMBRA1 has great plasticity

AMBRA1 as a central regulatory hub

RNA cryo-EM of the stem loop 5 domain from the 5’ UTR of Coronaviridae

Lily Xu, Stanford University, USA

SL5 is a 4-way junction, how these helixes stack together? 3D structure

SL5 folds independently from SL6

T-shape is conserved in Sarbecovirus SL5

BtCoV-HKU5 SL5 displays a different conformation from SARS-CoV-2 SL5

but MERS-CoV SL5 is similar to BtCoV-HKU5 SL5

same juction geometry, new tertiary interactions

Juction geometry is not conserved for HCoV-NL63 SL5