4GHQ | pdb_00004ghq

Crystal structure of EV71 3C proteinase

• PDB DOI: https://doi.org/10.2210/pdb4GHQ/pdb

• Classification: HYDROLASE
• Organism(s): Enterovirus A71
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-08 Released: 2013-06-26 
• Deposition Author(s): Chen, C., Wu, C., Cai, Q., Li, N., Peng, X., Cai, Y., Yin, K., Chen, X., Wang, X., Zhang, R., Liu, L., Chen, S., Li, J., Lin, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.272 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structures of Enterovirus 71 3C proteinase (strain E2004104-TW-CDC) and its complex with rupintrivir

Wu, C., Cai, Q., Chen, C., Li, N., Peng, X., Cai, Y., Yin, K., Chen, X., Wang, X., Zhang, R., Liu, L., Chen, S., Li, J., Lin, T.

(2013) Acta Crystallogr D Biol Crystallogr 69: 866-871

• PubMed: 23633597 
• DOI: https://doi.org/10.1107/S0907444913002862
• Primary Citation Related Structures: 
  4GHQ, 4GHT


• PubMed Abstract: 
  

  The crystal structure of 3C proteinase (3C(pro)) from Enterovirus 71 (EV71) was determined in space group C2221 to 2.2 Å resolution. The fold was similar to that of 3C(pro) from other picornaviruses, but the difference in the β-ribbon reported in a previous structure was not observed. This β-ribbon was folded over the substrate-binding cleft and constituted part of the essential binding sites for interaction with the substrate. The structure of its complex with rupintrivir (AG7088), a peptidomimetic inhibitor, was also characterized in space group P212121 to 1.96 Å resolution. The inhibitor was accommodated without any spatial hindrance despite the more constricted binding site; this was confirmed by functional assays, in which the inhibitor showed comparable potency towards EV71 3C(pro) and human rhinovirus 3C(pro), which is the target that rupintrivir was designed against.

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Organizational Affiliation: 
• State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.39 kDa 
• Atom Count: 1,495 
• Modeled Residue Count: 181 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C proteinase	A	192	Enterovirus A71	Mutation(s): 0  EC: 3.4.22.28
UniProt
Find proteins for A9XG43 (Human enterovirus 71) Explore A9XG43  Go to UniProtKB:  A9XG43

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.272 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.559	α = 90
b = 64.347	β = 90
c = 75.282	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Chen, C., Wu, C., Cai, Q., Li, N., Peng, X., Cai, Y., Yin, K., Chen, X., Wang, X., Zhang, R., Liu, L., Chen, S., Li, J., Lin, T.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description