9IOQ | pdb_00009ioq

Crystal structure of CapE bound cUA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Cyclic-dinucleotide-induced filamentous assembly of phospholipases governs broad CBASS immunity.

Wang, J.Li, Z.Lang, H.Fu, W.Gao, Y.Yin, S.Sun, P.Li, Z.Huang, J.Liu, S.Zhu, Y.Sun, F.Li, D.Gao, P.

(2025) Cell 188: 3744-3756.e16

  • DOI: https://doi.org/10.1016/j.cell.2025.04.022
  • Primary Citation Related Structures: 
    9IOM, 9ION, 9IOP, 9IOQ

  • PubMed Abstract: 

    Cyclic-oligonucleotide-based antiphage signaling systems (CBASS), a widespread antiviral bacterial immune system homologous to the mammalian cGAS-STING pathway, synthesizes cyclic nucleotide signals and triggers effector proteins to induce cell death and prevent viral propagation. Among various CBASS effectors, phospholipase effectors are the first to be discovered and are one of the most widespread families that sense cyclic dinucleotides to degrade cell membrane phospholipids. Here, we report that CBASS phospholipases assemble from a dimeric inactive state into active higher-order filamentous oligomers upon sensing cyclic dinucleotides. Using a combined approach of cryo-electron microscopy and X-ray crystallography, we have determined the structures of CBASS phospholipase in the inactive dimeric state, the cyclic-dinucleotide-bound active higher-order state, and the substrate-analog-bound catalytic mimicry state, thereby visualizing the complete conformational reorganization process. Complemented by functional assays of intermolecular binding, phospholipase enzymatic activity, in vitro membrane disruption, and in vivo antiphage efficiency, our work elucidates the mechanisms of assembly and activation of CBASS phospholipases.


  • Organizational Affiliation
    • Department of Radiology, Zhuhai People's Hospital, The Affiliated Hospital of Beijing Institute of Technology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.

Macromolecule Content 

  • Total Structure Weight: 36.04 kDa 
  • Atom Count: 2,546 
  • Modeled Residue Count: 312 
  • Deposited Residue Count: 320 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cUMP-AMP-activated phospholipase320Escherichia coliMutation(s): 0 
Gene Names: capE
EC: 3.1.1.32
UniProt
Find proteins for Q6XGD4 (Escherichia coli)
Explore Q6XGD4 
Go to UniProtKB:  Q6XGD4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XGD4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AEP
(Subject of Investigation/LOI)

Query on A1AEP



Download:Ideal Coordinates CCD File
B [auth A]3'3'-cUMP-AMP
C19 H23 N7 O14 P2
CYVLWDUVMGUTIY-KPKSGTNCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.942α = 90
b = 88.942β = 90
c = 82.312γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
Cootmodel building
PHENIXphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Database references