8JCE

Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GpppAmU


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Chikungunya virus nonstructural protein 1 is a versatile RNA capping and decapping enzyme.

Law, M.C.Y.Zhang, K.Tan, Y.B.Nguyen, T.M.Luo, D.

(2023) J Biol Chem 299: 105415-105415

  • DOI: https://doi.org/10.1016/j.jbc.2023.105415
  • Primary Citation of Related Structures:  
    8JCE

  • PubMed Abstract: 

    Chikungunya virus (CHIKV) nonstructural protein 1 (nsP1) contains both the N7-guanine methyltransferase and guanylyltransferase activities and catalyzes the 5' end cap formation of viral RNAs. To further understand its catalytic activity and role in virus-host interaction, we demonstrate that purified recombinant CHIKV nsP1 can reverse the guanylyl transfer reaction and remove the m 7 GMP from a variety of capped RNA substrates including host mRNAs. We then provide the structural basis of this function with a high-resolution cryo-EM structure of nsP1 in complex with the unconventional cap-1 substrate RNA m 7 GpppA m U. We show that the 5'ppRNA species generated by decapping can trigger retinoic acid-inducible gene I-mediated interferon response. We further demonstrate that the decapping activity is conserved among the alphaviral nsP1s. To our knowledge, this is a new mechanism through which alphaviruses activate the antiviral immune response. This decapping activity could promote cellular mRNA degradation and facilitate viral gene expression, which is functionally analogous to the cap-snatching mechanism by influenza virus.


  • Organizational Affiliation

    Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA-capping enzyme nsP1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
552Chikungunya virus strain S27-African prototypeMutation(s): 1 
EC: 2.1.1 (PDB Primary Data), 2.7.7 (PDB Primary Data)
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype))
Explore Q8JUX6 
Go to UniProtKB:  Q8JUX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JUX6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YG4 (Subject of Investigation/LOI)
Query on YG4

Download Ideal Coordinates CCD File 
BA [auth D]
DB [auth K]
FA [auth E]
HB [auth L]
JA [auth F]
BA [auth D],
DB [auth K],
FA [auth E],
HB [auth L],
JA [auth F],
NA [auth G],
O [auth A],
RA [auth H],
T [auth B],
VA [auth I],
X [auth C],
ZA [auth J]
[(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C31 H46 N12 O25 P4
POOGENYSODSFCS-SWDLWUBYSA-N
SAH
Query on SAH

Download Ideal Coordinates CCD File 
AA [auth D]
CB [auth K]
EA [auth E]
GB [auth L]
IA [auth F]
AA [auth D],
CB [auth K],
EA [auth E],
GB [auth L],
IA [auth F],
MA [auth G],
N [auth A],
QA [auth H],
S [auth B],
UA [auth I],
W [auth C],
YA [auth J]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BB [auth K]
DA [auth E]
FB [auth L]
HA [auth F]
LA [auth G]
BB [auth K],
DA [auth E],
FB [auth L],
HA [auth F],
LA [auth G],
M [auth A],
PA [auth H],
R [auth B],
TA [auth I],
V [auth C],
XA [auth J],
Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth K]
CA [auth E]
EB [auth L]
GA [auth F]
KA [auth G]
AB [auth K],
CA [auth E],
EB [auth L],
GA [auth F],
KA [auth G],
OA [auth H],
P [auth A],
Q [auth B],
SA [auth I],
U [auth C],
WA [auth J],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references