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 9X6C | pdb_00009x6c

crystal structure of an ATP bound anti-phage protein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 
    0.237 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Structural and functional insights into QueC-family protein in QatABCD anti-phage system.

Gao, Z., Li, F., Wang, H., Liu, X., Li, N., Xiong, W., Ma, W., Sun, D., Yan, D., Ma, Q., Xu, L., Zhang, Y.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-77369-4
  • Primary Citation Related Structures: 
    9WVJ, 9X6C

  • PubMed Abstract: 

    QatABCD is a widespread prokaryotic anti-phage defense system comprising four protein components, out of which QatC, a QueC-family protein is the signature component. QueC family proteins are nucleoside biosynthesis enzymes involved in the biosynthesis of queuosine, a 7-deazaguanine derivative. Recently, QueC-family proteins were shown to catalyze a deazaguanylation protein-nucleobase conjugation reaction in type IV CBASS antiphage defense. However, the mechanism of QatABCD, even the function of QatC in this system, remains unclear. Here, we demonstrate that QatBCD forms a complex in which QatD is highly flexible. Crystal structures of the QatBC complex in apo and ATP-bound form support a shared role for QueC-family proteins in targeting protein substrates for N-terminal modification as in type IV CBASS. We show that the QatB N-terminal loop, its binding with QatC and QatC catalytic site are essential for QatABCD defense in vivo, suggesting a modification might occur analogous to CBASS. These findings provide structural and functional insights into QueC-family protein in QatABCD system, suggesting the conserved mechanisms and critical roles of QueC-family in prokaryotic immunity.


  • Organizational Affiliation: 
    • State Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 81.74 kDa 
  • Atom Count: 5,572 
  • Modeled Residue Count: 723 
  • Deposited Residue Count: 745 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
7-cyano-7-deazaguanine synthaseA [auth B]471Escherichia coliMutation(s): 0 
Gene Names: CIG67_01895
UniProt
Find proteins for A0A4Q0WMG2 (Escherichia coli)
Explore A0A4Q0WMG2 
Go to UniProtKB:  A0A4Q0WMG2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Q0WMG2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF5610 domain-containing proteinB [auth D]274Escherichia coliMutation(s): 0 
Gene Names: CALFYP1_01022
UniProt
Find proteins for A0A6N2XJ30 (Citrobacter amalonaticus)
Explore A0A6N2XJ30 
Go to UniProtKB:  A0A6N2XJ30
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6N2XJ30
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free:  0.237 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.53α = 90
b = 120.43β = 90
c = 121.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-16
    Type: Initial release
  • Version 1.1: 2026-10-21
    Changes: Database references