Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 136.19 kDa 
• Atom Count: 9381 
• Modelled Residue Count: 1184 
• Deposited Residue Count: 1202 
• Unique protein chains: 2

5YIK

Structure of a Legionella effector with its substrate

• PDB DOI: 10.2210/pdb5YIK/pdb

• Classification: TRANSFERASE/PROTEIN BINDING
• Organism(s): Legionella pneumophila, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-05 Released: 2018-05-30 
• Deposition Author(s): Feng, Y., Dong, Y., Liu, Z.
• Funding Organization(s): National Science Foundation (China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

Structural basis of ubiquitin modification by the Legionella effector SdeA.

Dong, Y., Mu, Y., Xie, Y., Zhang, Y., Han, Y., Zhou, Y., Wang, W., Liu, Z., Wu, M., Wang, H., Pan, M., Xu, N., Xu, C.Q., Yang, M., Fan, S., Deng, H., Tan, T., Liu, X., Liu, L., Li, J., Wang, J., Fang, X., Feng, Y.

(2018) Nature 557: 674-678

• PubMed: 29795342 
• DOI: 10.1038/s41586-018-0146-7
• Primary Citation of Related Structures:  
  5YIJ, 5YIK, 5YIM


• PubMed Abstract: 
  

Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.

---

Organizational Affiliation: 

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SdeA	A	968	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for Q6RCR0 (Legionella pneumophila) Explore Q6RCR0  Go to UniProtKB:  Q6RCR0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin	B [auth C], C [auth D], D [auth F]	78	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.846	α = 90
b = 145.893	β = 104.46
c = 104.088	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-10-05 
• Released Date: 2018-05-30 
Deposition Author(s): Feng, Y., Dong, Y., Liu, Z.

---

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31670766

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references