8ST8 | pdb_00008st8

Structure of E3 ligase SopA bound to ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb8ST8/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-09 Released: 2023-07-12 
• Deposition Author(s): Franklin, T.G., Pruneda, J.N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Models: experimental

Literature

Bacterial ligases reveal fundamental principles of polyubiquitin specificity.

Franklin, T.G., Brzovic, P.S., Pruneda, J.N.

(2023) Mol Cell 83: 4538-4554.e4

• PubMed: 38091999 
• DOI: https://doi.org/10.1016/j.molcel.2023.11.017
• Primary Citation Related Structures: 
  8ST7, 8ST8, 8ST9


• PubMed Abstract: 
  

  Homologous to E6AP C terminus (HECT) E3 ubiquitin (Ub) ligases direct substrates toward distinct cellular fates dictated by the specific form of monomeric or polymeric Ub (polyUb) signal attached. How polyUb specificity is achieved has been a long-standing mystery, despite extensive study in various hosts, ranging from yeast to human. The bacterial pathogens enterohemorrhagic Escherichia coli and Salmonella Typhimurium encode outlying examples of "HECT-like" (bHECT) E3 ligases, but commonalities to eukaryotic HECT (eHECT) mechanism and specificity had not been explored. We expanded the bHECT family with examples in human and plant pathogens. Three bHECT structures in primed, Ub-loaded states resolved key details of the entire Ub ligation process. One structure provided a rare glimpse into the act of ligating polyUb, yielding a means to rewire polyUb specificity of both bHECT and eHECT ligases. Studying this evolutionarily distinct bHECT family has revealed insight into the function of key bacterial virulence factors as well as fundamental principles underlying HECT-type Ub ligation.

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Organizational Affiliation: 
• Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.59 kDa 
• Atom Count: 2,383 
• Modeled Residue Count: 270 
• Deposited Residue Count: 272 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase SopA	A	197	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: sopA, STM2066 EC: 2.3.2.26
UniProt
Find proteins for Q8ZNR3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZNR3  Go to UniProtKB:  Q8ZNR3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	75	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AYE	C [auth A]	prop-2-en-1-amine C3 H7 N VVJKKWFAADXIJK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.893	α = 90
b = 63.644	β = 90
c = 81.409	γ = 90

Software Package:

Software Name	Purpose
Web-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Franklin, T.G., Pruneda, J.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM142486

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references
• Version 1.2: 2024-01-03
  Changes: Database references