5BZ0 | pdb_00005bz0

Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb5BZ0/pdb

• Classification: HYDROLASE/PROTEIN BINDING
• Organism(s): Avian infectious bronchitis virus (strain Beaudette), Bos taurus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-06-11 Released: 2016-06-15 
• Deposition Author(s): Kong, L.Y., Yan, L.M., Zhang, Y., Rao, Z.H.
• Funding Organization(s): National Natural Science Foundation of China, National Major Project (973 Program), Tsinghua University Initiative Scientific Research Program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin

Kong, L.Y., Yan, L.M., Zhang, Y., Rao, Z.H.

To be published.

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: 43.62 kDa 
• Atom Count: 2,854 
• Modeled Residue Count: 324 
• Deposited Residue Count: 389 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	313	Avian infectious bronchitis virus (strain Beaudette)	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for P0C6Y1 (Avian infectious bronchitis virus (strain Beaudette)) Explore P0C6Y1  Go to UniProtKB:  P0C6Y1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-40S ribosomal protein S27a	B	76	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P62992 (Bos taurus) Explore P62992  Go to UniProtKB:  P62992

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.058	α = 90
b = 74.812	β = 90
c = 95.502	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Kong, L.Y., Yan, L.M., Zhang, Y., Rao, Z.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81330036 and 81322023
National Major Project (973 Program)	China	2014CB542800
Tsinghua University Initiative Scientific Research Program	China	20141080146

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Structure summary