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 

• DOI: https://doi.org/10.1126/science.adx6053

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