6C3R | pdb_00006c3r

Cricket paralysis virus RNAi suppressor protein CrPV-1A

• PDB DOI: https://doi.org/10.2210/pdb6C3R/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Cricket paralysis virus Teleogryllus commodus/Australia/CrPVVIC/1968
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-10 Released: 2018-10-17 
• Deposition Author(s): Nayak, A., Kim, D.Y., Andino, R., Gross, J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.280 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability.

Nayak, A., Kim, D.Y., Trnka, M.J., Kerr, C.H., Lidsky, P.V., Stanley, D.J., Rivera, B.M., Li, K.H., Burlingame, A.L., Jan, E., Frydman, J., Gross, J.D., Andino, R.

(2018) Cell Host Microbe 24: 542-557.e9

• PubMed: 30308158 
• DOI: https://doi.org/10.1016/j.chom.2018.09.006
• Primary Citation Related Structures: 
  6C3R


• PubMed Abstract: 
  

  The dicistrovirus, Cricket paralysis virus (CrPV) encodes an RNA interference (RNAi) suppressor, 1A, which modulates viral virulence. Using the Drosophila model, we combined structural, biochemical, and virological approaches to elucidate the strategies by which CrPV-1A restricts RNAi immunity. The atomic resolution structure of CrPV-1A uncovered a flexible loop that interacts with Argonaute 2 (Ago-2), thereby inhibiting Ago-2 endonuclease-dependent immunity. Mutations disrupting Ago-2 binding attenuates viral pathogenesis in wild-type but not Ago-2-deficient flies. CrPV-1A also contains a BC-box motif that enables the virus to hijack a host Cul2-Rbx1-EloBC ubiquitin ligase complex, which promotes Ago-2 degradation and virus replication. Our study uncovers a viral-based dual regulatory program that restricts antiviral immunity by direct interaction with and modulation of host proteins. While the direct inhibition of Ago-2 activity provides an efficient mechanism to establish infection, the recruitment of a ubiquitin ligase complex enables CrPV-1A to amplify Ago-2 inactivation to restrict further antiviral RNAi immunity.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, South Korea.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA.
Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.58 kDa 
• Atom Count: 2,387 
• Modeled Residue Count: 282 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cricket paralysis virus 1A protein	A, B	141	Cricket paralysis virus Teleogryllus commodus/Australia/CrPVVIC/1968	Mutation(s): 0  Gene Names: ORF1 EC: 3.4.22 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q9IJX4 (Cricket paralysis virus (isolate Teleogryllus commodus/Australia/CrPVVIC/1968)) Explore Q9IJX4  Go to UniProtKB:  Q9IJX4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.280 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.854	α = 90
b = 52.117	β = 90
c = 111.43	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Nayak, A., Kim, D.Y., Andino, R., Gross, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI36178, AI40085
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI091575
Department of Defense (DOD, United States)	United States	DARPA Prophecy

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-05-01
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary