NP - RNA interaction
NP RNA binding intro
(Zinzula Baumeister BBRC 2020 PMID: 33039147) Both the NTD and the CTD participate in the packaging of RNA viral genome, whereas the IDRs are involved in modulating the RNA binding activity. Furthermore, assembly into a functional nucleocapsid is a result of the homo-oligomerization properties of its CTD [13]. 42-44
Shown RNA binding domains
RBD NP - RBD-RNA structure - RNA binding mechanism
central linker region OC43 - see (Huang Hou 2009 Protein Sci PMID: 19691129)
Structural data of NP upon RNA binding
Structure of RBD+CTD and RNA
35551296 /2022 : in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together.
provided an octameric model for the full-length N bound to RNA that is consistent with electron microscopy images of the N protein in the presence of RNA.
RBP of Nucleocapsid CoV2
of the RNA binding domain alone - see: XXXX
of the RNA binding domain with RNA - see: XXXX
mutational analysis of RNA binding - see: XXXX
RBP of other Nucleocapsid proteins
see: XXXX
CoV2 - C-terminal domain in RNA binding
NP CTD crystal/cryo structures
Cov2 - full-length protein - RNA binding
PMID: 36202211 - ribonucleosome
Cryo-EM of NP-RNA
Optical Tweezer experiments
PMID: 36533523 /2023 : Sequence of N domains in RNA binding
RNA binding and Phase separation
NP might bind to 5' and 3' of the RNA genome at the same time to initiate packaging
NP - binding to 5' and 3' RNA genome ends
NP - Chaperone Function
RNA unwinding activity of the RBD
also see: NP - chaperone function
Duplex destabilisation
PMID: 34197802 /2021
MHV RBD - TRS unwinding activity
(Grossoehme Giedroc 2009 JMB 19782089) employs aromatic amino acid nucleobase stacking interactions with a triple adenosine motif to mediate high-affinity binding to single-stranded RNAs containing the transcriptional regulatory sequence (TRS) or its complement (cTRS). Stoichiometric NTD fully unwinds a TRS-cTRS duplex that mimics a transiently formed transcription intermediate in viral subgenomic RNA synthesis. Mutation of the solvent-exposed Y127, positioned on the β-platform surface of our 1.75 Å structure, binds the TRS far less tightly and is severely crippled in its RNA unwinding activity. In contrast, the C-terminal domain (CTD) exhibits no RNA unwinding activity. Viruses harboring Y127A N mutation are strongly selected against and Y127A N does not support an accessory function in MHV replication. We propose that the helix melting activity of the coronavirus N protein NTD plays a critical accessory role in subgenomic RNA synthesis and other processes requiring RNA remodeling.