6I7P

Crystal structure of the full-length Zika virus NS5 protein (Human isolate Z1106033)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Supramolecular arrangement of the full-length Zika virus NS5.

Ferrero, D.S.Ruiz-Arroyo, V.M.Soler, N.Uson, I.Guarne, A.Verdaguer, N.

(2019) PLoS Pathog 15: e1007656-e1007656

  • DOI: 10.1371/journal.ppat.1007656
  • Primary Citation of Related Structures:  
    6I7P, 5M2X, 5M2Z

  • PubMed Abstract: 
  • Zika virus (ZIKV), a member of the Flaviviridae family, has emerged as a major public health threat, since ZIKV infection has been connected to microcephaly and other neurological disorders. Flavivirus genome replication is driven by NS5, an RNA-dependent RNA polymerase (RdRP) that also contains a N-terminal methyltransferase domain essential for viral mRNA capping ...

    Zika virus (ZIKV), a member of the Flaviviridae family, has emerged as a major public health threat, since ZIKV infection has been connected to microcephaly and other neurological disorders. Flavivirus genome replication is driven by NS5, an RNA-dependent RNA polymerase (RdRP) that also contains a N-terminal methyltransferase domain essential for viral mRNA capping. Given its crucial roles, ZIKV NS5 has become an attractive antiviral target. Here, we have used integrated structural biology approaches to characterize the supramolecular arrangement of the full-length ZIKV NS5, highlighting the assembly and interfaces between NS5 monomers within a dimeric structure, as well as the dimer-dimer interactions to form higher order fibril-like structures. The relative orientation of each monomer within the dimer provides a model to explain the coordination between MTase and RdRP domains across neighboring NS5 molecules and mutational studies underscore the crucial role of the MTase residues Y25, K28 and K29 in NS5 dimerization. The basic residue K28 also participates in GTP binding and competition experiments indicate that NS5 dimerization is disrupted at high GTP concentrations. This competition represents a first glimpse at a molecular level explaining how dimerization might regulate the capping process.


    Organizational Affiliation

    Structural Biology Unit, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS5A, B, C, D, E, F914Zika virusMutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
AA [auth E], FA [auth F], G [auth A], L [auth B], P [auth C], T [auth D]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth E] , CA [auth E] , GA [auth F] , H [auth A] , HA [auth F] , I [auth A] , IA [auth F] , JA [auth F] , 
BA [auth E],  CA [auth E],  GA [auth F],  H [auth A],  HA [auth F],  I [auth A],  IA [auth F],  JA [auth F],  M [auth B],  N [auth B],  Q [auth C],  U [auth D],  V [auth D],  W [auth D],  X [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth E] , EA [auth E] , J [auth A] , K [auth A] , KA [auth F] , LA [auth F] , O [auth B] , R [auth C] , 
DA [auth E],  EA [auth E],  J [auth A],  K [auth A],  KA [auth F],  LA [auth F],  O [auth B],  R [auth C],  S [auth C],  Y [auth D],  Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.06α = 90
b = 192.06β = 90
c = 407.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and CompetitivenessSpainBIO2014-54588
Spanish Ministry of Economy and CompetitivenessSpainMDM-2014-0435

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations