5NFY

SARS-CoV nsp10/nsp14 dynamic complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA.

Ferron, F.Subissi, L.Silveira De Morais, A.T.Le, N.T.T.Sevajol, M.Gluais, L.Decroly, E.Vonrhein, C.Bricogne, G.Canard, B.Imbert, I.

(2018) Proc Natl Acad Sci U S A 115: E162-E171

  • DOI: 10.1073/pnas.1718806115
  • Primary Citation of Related Structures:  
    5NFY

  • PubMed Abstract: 
  • Coronaviruses (CoVs) stand out among RNA viruses because of their unusually large genomes (∼30 kb) associated with low mutation rates. CoVs code for nsp14, a bifunctional enzyme carrying RNA cap guanine N7-methyltransferase (MTase) and 3'-5' exoribonuclease (ExoN) activities ...

    Coronaviruses (CoVs) stand out among RNA viruses because of their unusually large genomes (∼30 kb) associated with low mutation rates. CoVs code for nsp14, a bifunctional enzyme carrying RNA cap guanine N7-methyltransferase (MTase) and 3'-5' exoribonuclease (ExoN) activities. ExoN excises nucleotide mismatches at the RNA 3'-end in vitro, and its inactivation in vivo jeopardizes viral genetic stability. Here, we demonstrate for severe acute respiratory syndrome (SARS)-CoV an RNA synthesis and proofreading pathway through association of nsp14 with the low-fidelity nsp12 viral RNA polymerase. Through this pathway, the antiviral compound ribavirin 5'-monophosphate is significantly incorporated but also readily excised from RNA, which may explain its limited efficacy in vivo. The crystal structure at 3.38 Å resolution of SARS-CoV nsp14 in complex with its cofactor nsp10 adds to the uniqueness of CoVs among RNA viruses: The MTase domain presents a new fold that differs sharply from the canonical Rossmann fold.


    Organizational Affiliation

    Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 13009 Marseille, France; isabelle.imbert@univ-amu.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyprotein 1abA, B, C, D534SARS coronavirus Frankfurt 1Mutation(s): 0 
EC: 2.7.7.48 (UniProt), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt)
Find proteins for Q1T6X8 (SARS coronavirus Frankfurt 1)
Explore Q1T6X8 
Go to UniProtKB:  Q1T6X8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyprotein 1abE [auth M], F [auth N], G [auth O], H [auth P]138SARS coronavirus Frankfurt 1Mutation(s): 0 
EC: 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt)
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth A], M [auth A], T [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth N] , BA [auth O] , CA [auth O] , DA [auth P] , EA [auth P] , I [auth A] , J [auth A] , K [auth A] , 
AA [auth N],  BA [auth O],  CA [auth O],  DA [auth P],  EA [auth P],  I [auth A],  J [auth A],  K [auth A],  N [auth B],  O [auth B],  P [auth B],  Q [auth C],  R [auth C],  S [auth C],  U [auth D],  V [auth D],  W [auth D],  X [auth M],  Y [auth M],  Z [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.881α = 90
b = 189.786β = 90
c = 196.245γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
AutoPROCdata collection
autoSHARPphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionFrancegrant agreement 260644

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations