8TYX

Structure of a bacterial Ubl-deubiquitinase complex (form 1)

• PDB DOI: https://doi.org/10.2210/pdb8TYX/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Ensifer aridi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-26 Released: 2024-06-12 
• Deposition Author(s): Ye, Q., Gong, M., Corbett, K.D.
• 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: 1.36 Å
• R-Value Free: 0.180 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Starting Model: in silico

Literature

A eukaryotic-like ubiquitination system in bacterial antiviral defence

Chambers, L.R., Ye, Q., Cai, J., Gong, M., Ledvina, H.E., Zhou, H., Whiteley, A.T., Suhandynata, R.T., Corbett, K.D.

(2024) Nature 

• DOI: https://doi.org/10.1038/s41586-024-07730-4

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 28.4 kDa 
• Atom Count: 2,332 
• Modelled Residue Count: 244 
• Deposited Residue Count: 260 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubl(BilA)	A	98	Ensifer aridi	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DUB(BilC) E33A Mutant	B	162	Ensifer aridi	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.180 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: I 2 2 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/1039

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.338	α = 90
b = 64.69	β = 90
c = 141.691	γ = 90

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: 2024-06-12 
Deposition Author(s): Ye, Q., Gong, M., Corbett, K.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM144121

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 1.1: 2024-07-17
  Changes: Database references