8K5Q | pdb_00008k5q

Crystal structure of YajQ STM0435 with c-di-GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

A c-di-GMP binding effector STM0435 modulates flagellar motility and pathogenicity in Salmonella

Dai , Y.Liu , R.Yue , Y.Song , N.Jia , H.Ma , Z.Gao , X.Zhang , M.Yuan , X.Liu , Q.Liu , X.Li , B.Wang , W.

(2024) Virulence 15: 2331265

  • DOI: https://doi.org/10.1080/21505594.2024.2331265
  • Primary Citation Related Structures: 
    8K4I, 8K5Q

  • PubMed Abstract: 

    Flagella play a crucial role in the invasion process of Salmonella and function as a significant antigen that triggers host pyroptosis. Regulation of flagellar biogenesis is essential for both pathogenicity and immune escape of Salmonella . We identified the conserved and unknown function protein STM0435 as a new flagellar regulator. The ∆ stm0435 strain exhibited higher pathogenicity in both cellular and animal infection experiments than the wild-type Salmonella . Proteomic and transcriptomic analyses demonstrated dramatic increases in almost all flagellar genes in the ∆ stm0435 strain compared to wild-type Salmonella . In a surface plasmon resonance assay, purified STM0435 protein-bound c-di-GMP had an affinity of ~8.383 µM. The crystal structures of apo-STM0435 and STM0435&c-di-GMP complex were determined. Structural analysis revealed that R33, R137, and D138 of STM0435 were essential for c-di-GMP binding. A Salmonella with STM1987 (GGDEF protein) or STM4264 (EAL protein) overexpression exhibits completely different motility behaviours, indicating that the binding of c-di-GMP to STM0435 promotes its inhibitory effect on Salmonella flagellar biogenesis.


  • Organizational Affiliation
    • Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.

Macromolecule Content 

  • Total Structure Weight: 19.73 kDa 
  • Atom Count: 1,450 
  • Modeled Residue Count: 163 
  • Deposited Residue Count: 163 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YajQ163Salmonella enterica subsp. enterica serovar Typhimurium str. 14028SMutation(s): 0 
Gene Names: yajQ
UniProt
Find proteins for Q8ZRC9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZRC9 
Go to UniProtKB:  Q8ZRC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZRC9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E
(Subject of Investigation/LOI)

Query on C2E



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.984α = 90
b = 51.697β = 90
c = 126.267γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

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)China32170034

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release