7PKU

Structure of SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a.

Bessa, L.M.Guseva, S.Camacho-Zarco, A.R.Salvi, N.Maurin, D.Perez, L.M.Botova, M.Malki, A.Nanao, M.Jensen, M.R.Ruigrok, R.W.H.Blackledge, M.

(2022) Sci Adv 8: eabm4034-eabm4034

  • DOI: 10.1126/sciadv.abm4034
  • Primary Citation of Related Structures:  
    7PKU

  • PubMed Abstract: 
  • The processes of genome replication and transcription of SARS-CoV-2 represent important targets for viral inhibition. Betacoronaviral nucleoprotein (N) is a highly dynamic cofactor of the replication-transcription complex (RTC), whose function depends on an essential interaction with the amino-terminal ubiquitin-like domain of nsp3 (Ubl1) ...

    The processes of genome replication and transcription of SARS-CoV-2 represent important targets for viral inhibition. Betacoronaviral nucleoprotein (N) is a highly dynamic cofactor of the replication-transcription complex (RTC), whose function depends on an essential interaction with the amino-terminal ubiquitin-like domain of nsp3 (Ubl1). Here, we describe this complex (dissociation constant - 30 to 200 nM) at atomic resolution. The interaction implicates two linear motifs in the intrinsically disordered linker domain (N3), a hydrophobic helix ( 219 LALLLLDRLNQL 230 ) and a disordered polar strand ( 243 GQTVTKKSAAEAS 255 ), that mutually engage to form a bipartite interaction, folding N3 around Ubl1. This results in substantial collapse in the dimensions of dimeric N, forming a highly compact molecular chaperone, that regulates binding to RNA, suggesting a key role of nsp3 in the association of N to the RTC. The identification of distinct linear motifs that mediate an important interaction between essential viral factors provides future targets for development of innovative strategies against COVID-19.


    Organizational Affiliation

    Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA96Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: ORF1ab
EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
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Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinB73Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)European UnionSARS2NUCLEOPROTEIN
European Research Council (ERC)European UnionDynamicAssemblies

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references