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

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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