3H5X

Crystal Structure of 2'-amino-2'-deoxy-cytidine-5'-triphosphate bound to Norovirus GII RNA polymerase

• PDB DOI: https://doi.org/10.2210/pdb3H5X/pdb
• NAKB: 3H5X

• Classification: Transferase/RNA
• Organism(s): Norwalk virus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-22 Released: 2009-05-19 
• Deposition Author(s): Zamyatkin, D.F., Parra, F., Machin, A., Grochulski, P., Ng, K.K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.246 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Binding of 2'-amino-2'-deoxycytidine-5'-triphosphate to norovirus polymerase induces rearrangement of the active site.

Zamyatkin, D.F., Parra, F., Machin, A., Grochulski, P., Ng, K.K.

(2009) J Mol Biol 390: 10-16

• PubMed: 19426741 
• DOI: https://doi.org/10.1016/j.jmb.2009.04.069
• Primary Citation of Related Structures:  
  3H5X, 3H5Y


• PubMed Abstract: 
  

  Crystal structures of a genogroup II.4 human norovirus polymerase bound to an RNA primer-template duplex and the substrate analogue 2'-amino-2'-deoxycytidine-5'-triphosphate have been determined to 1.8 A resolution. The alteration of the substrate-binding site that is required to accommodate the 2'-amino group leads to a rearrangement of the polymerase active site and a disruption of the coordination shells of the active-site metal ions. The mode of binding seen for 2'-amino-2'-deoxycytidine-5'-triphosphate suggests a novel molecular mechanism of inhibition that may be exploited for the design of inhibitors targeting viral RNA polymerases.

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Organizational Affiliation: 

Department of Biological Sciences and Alberta Ingenuity Centre for Carbohydrate Science, University of Calgary, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 63.33 kDa 
• Atom Count: 4,532 
• Modelled Residue Count: 486 
• Deposited Residue Count: 527 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA dependent RNA polymerase	A	510	Norwalk virus	Mutation(s): 1  Gene Names: polymerase EC: 2.7.7.48
UniProt
Find proteins for Q70ET3 (Norwalk virus) Explore Q70ET3  Go to UniProtKB:  Q70ET3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'	B [auth P]	8	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3'	C [auth T]	9	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CSG	H [auth A]	2'-amino-2'-deoxycytidine 5'-(tetrahydrogen triphosphate) C9 H17 N4 O13 P3 WNVZQYHBHSLUHJ-XVFCMESISA-N
GOL	I [auth A], J [auth A], K [auth A], L [auth T]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth A], E [auth A], F [auth A], G [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.246 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.6	α = 90
b = 93.7	β = 90
c = 96.6	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Zamyatkin, D.F., Parra, F., Machin, A., Grochulski, P., Ng, K.K.S.

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description