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 8WCN | pdb_00008wcn

Cryo-EM structure of PAO1-ImcA with GMPCPP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WCN

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

Literature

A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa.

Zhan, X., Zhang, K., Wang, C., Fan, Q., Tang, X., Zhang, X., Wang, K., Fu, Y., Liang, H.

(2024) Nat Commun 15: 1860-1860

  • DOI: https://doi.org/10.1038/s41467-024-46149-3
  • Primary Citation Related Structures: 
    8WCN, 8WCT

  • PubMed Abstract: 

    Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous studies have conducted comprehensive analysis of c-di-GMP. However, the mechanisms by which certain environmental signals such as iron control intracellular c-di-GMP levels are unclear. Here, we show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein, IsmP, and a diguanylate cyclase, ImcA. Binding of iron to the CHASE4 domain of IsmP inhibits the IsmP-ImcA interaction, which leads to increased c-di-GMP synthesis by ImcA, thus promoting biofilm formation and reducing bacterial motility. Structural characterization of the apo-CHASE4 domain and its binding to iron allows us to pinpoint residues defining its specificity. In addition, the cryo-electron microscopy structure of ImcA in complex with a c-di-GMP analog (GMPCPP) suggests a unique conformation in which the compound binds to the catalytic pockets and to the membrane-proximal side located at the cytoplasm. Thus, our results indicate that a CHASE4 domain directly senses iron and modulates the crosstalk between c-di-GMP metabolic enzymes.


  • Organizational Affiliation: 
    • College of Life Sciences, Northwest University, Xi'an, ShaanXi, China.

Macromolecule Content 

  • Total Structure Weight: 104.79 kDa 
  • Atom Count: 6,086 
  • Modeled Residue Count: 757 
  • Deposited Residue Count: 922 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Diguanylate cyclase
A, B
461Pseudomonas aeruginosaMutation(s): 0 
Gene Names: DT376_18320
EC: 2.7.7.65
Membrane Entity: Yes 
UniProt
Find proteins for A0A072ZHL9 (Pseudomonas aeruginosa)
Explore A0A072ZHL9 
Go to UniProtKB:  A0A072ZHL9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A072ZHL9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection, Structure summary