5ULP

Structure of the NS5 methyltransferase from Zika bound to MS2042

• PDB DOI: https://doi.org/10.2210/pdb5ULP/pdb

• Classification: HYDROLASE
• Organism(s): Zika virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-25 Released: 2017-05-17 
• Deposition Author(s): Jain, R., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.199 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Development of a S-adenosylmethionine analog that intrudes the RNA-cap binding site of Zika methyltransferase.

Jain, R., Butler, K.V., Coloma, J., Jin, J., Aggarwal, A.K.

(2017) Sci Rep 7: 1632-1632

• PubMed: 28487506 
• DOI: https://doi.org/10.1038/s41598-017-01756-7
• Primary Citation of Related Structures:  
  5ULP


• PubMed Abstract: 
  

  The Zika virus (ZIKV) has emerged as a major health hazard. We present here a high resolution structure (1.55 Å) of ZIKV NS5 methyltransferase bound to a novel S-adenosylmethionine (SAM) analog in which a 4-fluorophenyl moiety substitutes for the methyl group. We show that the 4-fluorophenyl moiety extends into a portion of the RNA binding tunnel that typically contains the adenosine 2'OH of the RNA-cap moiety. Together, the new SAM analog and the high-resolution crystal structure are a step towards the development of antivirals against ZIKV and other flaviviruses.

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Organizational Affiliation: 

Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.84 kDa 
• Atom Count: 4,894 
• Modelled Residue Count: 524 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MRNA cap 0-1 NS5-type methyltransferase	A, B	268	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KB1	C [auth A], L [auth B]	5'-{[(3S)-3-amino-3-carboxypropyl][(4-fluorophenyl)methyl]amino}-5'-deoxyadenosine C21 H26 F N7 O5 UBYUMSGWGXUICY-SWQDORGXSA-N
IPA	J [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
URE	G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	K [auth A], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KB1	Binding MOAD:  5ULP	Kd: 2.43e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.199 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.989	α = 90
b = 111.231	β = 93.87
c = 77.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-17 
Deposition Author(s): Jain, R., Aggarwal, A.K.

Revision History  

• Version 1.0: 2017-05-17
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description