6KU8 | pdb_00006ku8

structure of HRV-C 3C protein with rupintrivir

• PDB DOI: https://doi.org/10.2210/pdb6KU8/pdb

• Classification: HYDROLASE
• Organism(s): Rhinovirus C
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-08-31 Released: 2020-03-25 
• Deposition Author(s): Zhu, L., Yuan, S.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.223 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 

Starting Model: experimental

Literature

Structure of the HRV-C 3C-Rupintrivir Complex Provides New Insights for Inhibitor Design.

Yuan, S., Fan, K., Chen, Z., Sun, Y., Hou, H., Zhu, L.

(2020) Virol Sin 35: 445-454

• PubMed: 32103448 
• DOI: https://doi.org/10.1007/s12250-020-00196-4
• Primary Citation Related Structures: 
  6KU7, 6KU8


• PubMed Abstract: 
  

  Human rhinoviruses (HRVs) are the predominant infectious agents for the common cold worldwide. The HRV-C species cause severe illnesses in children and are closely related to acute exacerbations of asthma. 3C protease, a highly conserved enzyme, cleaves the viral polyprotein during replication and assists the virus in escaping the host immune system. These key roles make 3C protease an important drug target. A few structures of 3Cs complexed with an irreversible inhibitor rupintrivir have been determined. These structures shed light on the determinants of drug specificity. Here we describe the structures of HRV-C15 3C in free and inhibitor-bound forms. The volume-decreased S1' subsite and half-closed S2 subsite, which were thought to be unique features of enterovirus A 3C proteases, appear in the HRV-C 3C protease. Rupintrivir assumes an "intermediate" conformation in the complex, which might open up additional avenues for the design of potent antiviral inhibitors. Analysis of the features of the three-dimensional structures and the amino acid sequences of 3C proteases suggest new applications for existing drugs.

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Organizational Affiliation: 
• CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA.
Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China.
Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China.
Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China.
Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China. [e-mail].
Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China. [e-mail].
CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.21 kDa 
• Atom Count: 1,559 
• Modeled Residue Count: 177 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	183	Rhinovirus C	Mutation(s): 0  EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15)) Explore E5D8F2  Go to UniProtKB:  E5D8F2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG7 (Subject of Investigation/LOI)	B [auth A]	4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER C31 H41 F N4 O7 LMIUALQNZXJHOG-IFILWLFVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.223 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.903	α = 90
b = 95.626	β = 90
c = 98.853	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Zhu, L., Yuan, S.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31800145

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description