9NLG | pdb_00009nlg

CBASS Pseudomonas syringae Cap5 tetramer with 3'2'-c-GAMP cyclic dinucleotide ligand (His56Ala mutant without Mg2+ ions)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.181 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Mechanism of DNA degradation by CBASS Cap5 endonuclease immune effector.

Rechkoblit, O.Sciaky, D.Ni, M.Li, Y.Kottur, J.Fang, G.Aggarwal, A.K.

(2025) Nat Commun 16: 5243-5243

  • DOI: https://doi.org/10.1038/s41467-025-60484-z
  • Primary Citation Related Structures: 
    9DIF, 9DIH, 9NLG

  • PubMed Abstract: 

    Bacterial CBASS immune defense systems commonly kill virally infected cells by degrading genomic DNA in a form of cell suicide or abortive infection. We present a high-resolution structure of the CBASS effector Cap5, activated by a cyclic nucleotide, in the act of digesting DNA via tetrameric HNH endonuclease domains. Two HNH domains are in a catalytically active state for cleavage of the DNA strands, whereas the other two HNH domains are in a topologically distinct catalytically inactive state for simply DNA binding. The four HNH domains track one face of the DNA and mark an enzyme that acts as a stand-alone non-specific nuclease. We also show that chromosomally encoded CBASS Cap5 can be extrinsically activated by a cyclic nucleotide, as a step towards potential antibiotics.


  • Organizational Affiliation
    • Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. olga.rechkoblit@mssm.edu.

Macromolecule Content 

  • Total Structure Weight: 173.86 kDa 
  • Atom Count: 13,036 
  • Modeled Residue Count: 1,456 
  • Deposited Residue Count: 1,552 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HNH endonuclease
A, B, C, D
388Pseudomonas syringaeMutation(s): 1 
UniProt
Find proteins for A0A2P0QGK5 (Pseudomonas syringae pv. actinidiae)
Explore A0A2P0QGK5 
Go to UniProtKB:  A0A2P0QGK5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P0QGK5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4UR
(Subject of Investigation/LOI)

Query on 4UR



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
K [auth C],
M [auth D]
3'2'-cGAMP
C20 H24 N10 O13 P2
FAFONCPHZLORMH-INFSMZHSSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
J [auth C],
L [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.181 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.564α = 63.4
b = 77.833β = 80.84
c = 80.989γ = 79.17
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

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 General Medical Sciences (NIH/NIGMS)United StatesR35-GM131780

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release