7TGQ | pdb_00007tgq

Zinc finger antiviral protein (ZAP) central domain bound to ADP-ribose

  • Classification: ANTIVIRAL PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-01-09 Released: 2022-02-02 
  • Deposition Author(s): Pornillos, O.P.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.273 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.238 (Depositor) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7TGQ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Poly(ADP-ribose) potentiates ZAP antiviral activity.

Xue, G.Braczyk, K.Goncalves-Carneiro, D.Dawidziak, D.M.Sanchez, K.Ong, H.Wan, Y.Zadrozny, K.K.Ganser-Pornillos, B.K.Bieniasz, P.D.Pornillos, O.

(2022) PLoS Pathog 18: e1009202-e1009202

  • DOI: https://doi.org/10.1371/journal.ppat.1009202
  • Primary Citation Related Structures: 
    7KZH, 7TGQ

  • PubMed Abstract: 

    Zinc-finger antiviral protein (ZAP), also known as poly(ADP-ribose) polymerase 13 (PARP13), is an antiviral factor that selectively targets viral RNA for degradation. ZAP is active against both DNA and RNA viruses, including important human pathogens such as hepatitis B virus and type 1 human immunodeficiency virus (HIV-1). ZAP selectively binds CpG dinucleotides through its N-terminal RNA-binding domain, which consists of four zinc fingers. ZAP also contains a central region that consists of a fifth zinc finger and two WWE domains. Through structural and biochemical studies, we found that the fifth zinc finger and tandem WWEs of ZAP combine into a single integrated domain that binds to poly(ADP-ribose) (PAR), a cellular polynucleotide. PAR binding is mediated by the second WWE module of ZAP and likely involves specific recognition of an adenosine diphosphate-containing unit of PAR. Mutation of the PAR binding site in ZAP abrogates the interaction in vitro and diminishes ZAP activity against a CpG-rich HIV-1 reporter virus and murine leukemia virus. In cells, PAR facilitates formation of non-membranous sub-cellular compartments such as DNA repair foci, spindle poles and cytosolic RNA stress granules. Our results suggest that ZAP-mediated viral mRNA degradation is facilitated by PAR, and provides a biophysical rationale for the reported association of ZAP with RNA stress granules.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America.

Macromolecule Content 

  • Total Structure Weight: 24.13 kDa 
  • Atom Count: 1,566 
  • Modeled Residue Count: 182 
  • Deposited Residue Count: 202 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger CCCH-type antiviral protein 1202Homo sapiensMutation(s): 0 
Gene Names: ZC3HAV1ZC3HDC2PRO1677
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z2W4 (Homo sapiens)
Explore Q7Z2W4 
Go to UniProtKB:  Q7Z2W4
PHAROS:  Q7Z2W4
GTEx:  ENSG00000105939 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z2W4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.273 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.238 (Depositor) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.958α = 90
b = 89.958β = 90
c = 52.807γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI150479
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54-AI150470

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description