Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 81.33 kDa 
• Atom Count: 5138 
• Modelled Residue Count: 642 
• Deposited Residue Count: 717 
• Unique protein chains: 2

6K2D

The crystal structure of GBP1 with LRR domain of IpaH9.8

• PDB DOI: 10.2210/pdb6K2D/pdb

• Classification: HYDROLASE/TRANSFERASE
• Organism(s): Homo sapiens, Shigella flexneri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-14 Released: 2019-06-12 
• Deposition Author(s): Ji, C.G., Xiao, J.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.287 
• R-Value Work: 0.240 
• R-Value Observed: 0.243 

Literature

Structural mechanism for guanylate-binding proteins (GBPs) targeting by the Shigella E3 ligase IpaH9.8.

Ji, C., Du, S., Li, P., Zhu, Q., Yang, X., Long, C., Yu, J., Shao, F., Xiao, J.Y.

(2019) PLoS Pathog 15: e1007876-e1007876

• PubMed: 31216343 
• DOI: 10.1371/journal.ppat.1007876
• Primary Citation of Related Structures:  
  6K1Z, 6K2D


• PubMed Abstract: 
  

The guanylate-binding proteins (GBPs) belong to the dynamin superfamily of GTPases and function in cell-autonomous defense against intracellular pathogens. IpaH9.8, an E3 ligase from the pathogenic bacterium Shigella flexneri, ubiquitinates a subset of GBPs and leads to their proteasomal degradation. Here we report the structure of a C-terminally truncated GBP1 in complex with the IpaH9.8 Leucine-rich repeat (LRR) domain. IpaH9.8LRR engages the GTPase domain of GBP1, and differences in the Switch II and α3 helix regions render some GBPs such as GBP3 and GBP7 resistant to IpaH9.8. Comparisons with other IpaH structures uncover interaction hot spots in their LRR domains. The C-terminal region of GBP1 undergoes a large rotation compared to previously determined structures. We further show that the C-terminal farnesylation modification also plays a role in regulating GBP1 conformation. Our results suggest a general mechanism by which the IpaH proteins target their cellular substrates and shed light on the structural dynamics of the GBPs.

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Organizational Affiliation: 

The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate-binding protein 1	A	481	Homo sapiens	Mutation(s): 0  Gene Names: GBP1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P32455 (Homo sapiens) Explore P32455  Go to UniProtKB:  P32455
PHAROS:  P32455

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase ipaH9.8	B	236	Shigella flexneri	Mutation(s): 0  Gene Names: ipaH9.8, CP0226, pWR501_0234, SFLP090 EC: 2.3.2.27
UniProt
Find proteins for Q8VSC3 (Shigella flexneri) Explore Q8VSC3  Go to UniProtKB:  Q8VSC3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.287 
• R-Value Work: 0.240 
• R-Value Observed: 0.243 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.736	α = 90
b = 211.736	β = 90
c = 56.975	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-05-14 
• Released Date: 2019-06-12 
Deposition Author(s): Ji, C.G., Xiao, J.Y.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Database references