6UEJ

Crystal structure of human zinc finger antiviral protein bound to RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences.

Meagher, J.L.Takata, M.Goncalves-Carneiro, D.Keane, S.C.Rebendenne, A.Ong, H.Orr, V.K.MacDonald, M.R.Stuckey, J.A.Bieniasz, P.D.Smith, J.L.

(2019) Proc.Natl.Acad.Sci.USA --: --

  • DOI: 10.1073/pnas.1913232116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Infection of animal cells by numerous viruses is detected and countered by a variety of means, including recognition of nonself nucleic acids. The zinc finger antiviral protein (ZAP) depletes cytoplasmic RNA that is recognized as foreign in mammalian ...

    Infection of animal cells by numerous viruses is detected and countered by a variety of means, including recognition of nonself nucleic acids. The zinc finger antiviral protein (ZAP) depletes cytoplasmic RNA that is recognized as foreign in mammalian cells by virtue of its elevated CG dinucleotide content compared with endogenous mRNAs. Here, we determined a crystal structure of a protein-RNA complex containing the N-terminal, 4-zinc finger human (h) ZAP RNA-binding domain (RBD) and a CG dinucleotide-containing RNA target. The structure reveals in molecular detail how hZAP is able to bind selectively to CG-rich RNA. Specifically, the 4 zinc fingers create a basic patch on the hZAP RBD surface. The highly basic second zinc finger contains a pocket that selectively accommodates CG dinucleotide bases. Structure guided mutagenesis, cross-linking immunoprecipitation sequencing assays, and RNA affinity assays show that the structurally defined CG-binding pocket is not required for RNA binding per se in human cells. However, the pocket is a crucial determinant of high-affinity, specific binding to CG dinucleotide-containing RNA. Moreover, variations in RNA-binding specificity among a panel of CG-binding pocket mutants quantitatively predict their selective antiviral activity against a CG-enriched HIV-1 strain. Overall, the hZAP RBD RNA structure provides an atomic-level explanation for how ZAP selectively targets foreign, CG-rich RNA.


    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109.,Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109.,Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065; pbieniasz@rockefeller.edu JanetSmith@umich.edu.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; pbieniasz@rockefeller.edu JanetSmith@umich.edu.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065.,Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065.,Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger CCCH-type antiviral protein 1
A
229Homo sapiensMutation(s): 0 
Gene Names: ZC3HAV1 (ZC3HDC2)
Find proteins for Q7Z2W4 (Homo sapiens)
Go to Gene View: ZC3HAV1
Go to UniProtKB:  Q7Z2W4
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*CP*G)-3')B3synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
B
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.211 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 123.090α = 90.00
b = 123.090β = 90.00
c = 40.670γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesU54 AI50470

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-27
    Type: Database references