9NTN | pdb_00009ntn

Structure of Cap10-CdnD complex containing NDG modification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.278 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history


Literature

Deazaguanylation is a nucleobase-protein conjugation required for type IV CBASS immunity.

Wassarman, D.R.Pfaff, P.Paulo, J.A.Gygi, S.P.Shokat, K.M.Kranzusch, P.J.

(2025) Science 389: 1347-1352

  • DOI: https://doi.org/10.1126/science.adx6053
  • Primary Citation of Related Structures:  
    9NTN, 9NTO

  • PubMed Abstract: 

    7-Deazapurines are nucleobase analogs essential for nucleic acid modifications in nearly all cellular life. In this study, we discovered a role for 7-deazapurines in protein modification within type IV cyclic oligonucleotide-based antiviral signaling system (CBASS) antiphage defense and defined functions for CBASS ancillary proteins Cap9 and Cap10 in nucleobase-protein conjugation. A structure of Cap10 revealed a transfer RNA transglycosylase family enzyme remodeled to bind a partner cGAS/DncV-like nucleotidyltransferase that is modified with an N-terminal 7-amido-7-deazaguanine (NDG) nucleobase. A structure of Cap9 explained how this QueC-like enzyme co-opts a 7-deazapurine biosynthetic reaction to install NDG. We show that Cap9, Cap10, and protein deazaguanylation are essential for host defense against phage infection. Our results define a 7-deazapurine protein modification and explain how nucleobase biosynthetic machinery has been repurposed for antiviral immunity.


  • Organizational Affiliation
    • Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cap10
A, B
332HyphomicrobialesMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CdnDC [auth G],
D [auth H]
320HyphomicrobialesMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.278 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.459α = 90
b = 82.92β = 90
c = 231.779γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
AutoProcessdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1DP2GM146250-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Database references
  • Version 1.2: 2025-10-08
    Changes: Database references