9NTO | pdb_00009nto

Structure of Cap9-CdnD complex containing NDG modification

• PDB DOI: https://doi.org/10.2210/pdb9NTO/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Hyphomicrobiales
• Expression System: Escherichia coli BW25113
• Mutation(s): No 


• Deposited: 2025-03-18 Released: 2025-05-07 
• Deposition Author(s): Wassarman, D.R., Pfaff, P., Paulo, J.A., Gygi, S.P., Shokat, K.M., Kranzusch, P.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

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

• PubMed: 40997174 
• DOI: https://doi.org/10.1126/science.adx6053
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 55.37 kDa 
• Atom Count: 3,743 
• Modeled Residue Count: 464 
• Deposited Residue Count: 511 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdnD	A	320	Hyphomicrobiales	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cap9	B	191	Hyphomicrobiales	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
ADN	F [auth B]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
2KA (Subject of Investigation/LOI)	D [auth A]	2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid C7 H6 N4 O3 XIUIRSLBMMTDSK-UHFFFAOYSA-N
ZN	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.664	α = 90
b = 58.219	β = 90
c = 89.228	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
AutoProcess	data processing
Coot	model building
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Wassarman, D.R., Pfaff, P., Paulo, J.A., Gygi, S.P., Shokat, K.M., Kranzusch, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1DP2GM146250-01

Revision History  

• 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