8J9B | pdb_00008j9b

LnaB-actin binary complex

• PDB DOI: https://doi.org/10.2210/pdb8J9B/pdb

• Classification: TRANSFERASE
• Organism(s): Oryctolagus cuniculus, Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-03 Released: 2024-05-08 
• Deposition Author(s): Chen, T.T., Ouyang, S.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.42 Å
• R-Value Free: 
  0.298 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.287 (Depositor), 0.290 (DCC) 

Starting Model: in silico

Literature

Legionella maintains host cell ubiquitin homeostasis by effectors with unique catalytic mechanisms.

Fu, J., Li, S., Guan, H., Li, C., Zhao, Y.B., Chen, T.T., Xian, W., Zhang, Z., Liu, Y., Guan, Q., Wang, J., Lu, Q., Kang, L., Zheng, S.R., Li, J., Cao, S., Das, C., Liu, X., Song, L., Ouyang, S., Luo, Z.Q.

(2024) Nat Commun 15: 5953-5953

• PubMed: 39009586 
• DOI: https://doi.org/10.1038/s41467-024-50311-2
• Primary Citation Related Structures: 
  8IPJ, 8IPW, 8J9B


• PubMed Abstract: 
  

  The intracellular bacterial pathogen Legionella pneumophila modulates host cell functions by secreting multiple effectors with diverse biochemical activities. In particular, effectors of the SidE family interfere with host protein ubiquitination in a process that involves production of phosphoribosyl ubiquitin (PR-Ub). Here, we show that effector LnaB converts PR-Ub into ADP-ribosylated ubiquitin, which is further processed to ADP-ribose and functional ubiquitin by the (ADP-ribosyl)hydrolase MavL, thus maintaining ubiquitin homeostasis in infected cells. Upon being activated by actin, LnaB also undergoes self-AMPylation on tyrosine residues. The activity of LnaB requires a motif consisting of Ser, His and Glu (SHxxxE) present in a large family of toxins from diverse bacterial pathogens. Thus, our study sheds light on the mechanisms by which a pathogen maintains ubiquitin homeostasis and identifies a family of enzymes capable of protein AMPylation.

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Organizational Affiliation: 
• Department of Respiratory Medicine, Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China.
Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.
Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Department of Microbiology, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
Department of Chemistry, Purdue University, West Lafayette, IN, USA.
College of Chemistry, Fuzhou University, Fuzhou, Fujian, China.
Department of Microbiology, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China. [e-mail].
Department of Respiratory Medicine, Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China. [e-mail].
Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China. [e-mail].
Department of Biological Sciences, Purdue University, West Lafayette, IN, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 20-mer - A12B8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 455.52 kDa 
• Atom Count: 26,804 
• Modeled Residue Count: 3,374 
• Deposited Residue Count: 4,014 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin gamma 1	A, B, C, D, E, F	375	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A8C6VAB1 (Naja naja) Explore A0A8C6VAB1  Go to UniProtKB:  A0A8C6VAB1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV secretion protein Dot	G [auth H], H [auth I], I [auth J], J [auth K]	441	Legionella pneumophila	Mutation(s): 0  Gene Names: C3927_12730

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.42 Å
• R-Value Free:  0.298 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.287 (Depositor), 0.290 (DCC) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.577	α = 90
b = 110.577	β = 90
c = 407.927	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Chen, T.T., Ouyang, S.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Database references, Structure summary