6PPO

Rhinovirus C15 complexed with domain I of receptor CDHR3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of rhinovirus C15a bound to its cadherin-related protein 3 receptor.

Sun, Y.Watters, K.Hill, M.G.Fang, Q.Liu, Y.Kuhn, R.J.Klose, T.Rossmann, M.G.Palmenberg, A.C.

(2020) Proc Natl Acad Sci U S A 117: 6784-6791

  • DOI: 10.1073/pnas.1921640117
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Infection by Rhinovirus-C (RV-C), a species of Picornaviridae Enterovirus , is strongly associated with childhood asthma exacerbations. Cellular binding and entry by all RV-C, which trigger these episodes, is mediated by the first ex ...

    Infection by Rhinovirus-C (RV-C), a species of Picornaviridae Enterovirus , is strongly associated with childhood asthma exacerbations. Cellular binding and entry by all RV-C, which trigger these episodes, is mediated by the first extracellular domain (EC1) of cadherin-related protein 3 (CDHR3), a surface cadherin-like protein expressed primarily on the apical surfaces of ciliated airway epithelial cells. Although recombinant EC1 is a potent inhibitor of viral infection, there is no molecular description of this protein or its binding site on RV-C. Here we present cryo-electron microscopy (EM) data resolving the EC1 and EC1+2 domains of human CDHR3 complexed with viral isolate C15a. Structure-suggested residues contributing to required interfaces on both EC1 and C15a were probed and identified by mutagenesis studies with four different RV-C genotypes. In contrast to most other rhinoviruses, which bind intercellular adhesion molecule 1 receptors via a capsid protein VP1-specific fivefold canyon feature, the CDHR3 EC1 contacts C15a, and presumably all RV-Cs, in a unique cohesive footprint near the threefold vertex, encompassing residues primarily from viral protein VP3, but also from VP1 and VP2. The EC1+2 footprint on C15a is similar to that of EC1 alone but shows that steric hindrance imposed by EC2 would likely prevent multiprotein binding by the native receptor at any singular threefold vertex. Definition of the molecular interface between the RV-Cs and their receptors provides new avenues that can be explored for potential antiviral therapies.


    Organizational Affiliation

    Institute for Molecular Virology, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706; acpalmen@wisc.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A
279Rhinovirus CMutation(s): 1 
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)
Find proteins for E5D8F2 (Rhinovirus C)
Go to UniProtKB:  E5D8F2

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP3
B
235Rhinovirus CMutation(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)
Find proteins for E5D8F2 (Rhinovirus C)
Go to UniProtKB:  E5D8F2

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2
C
265Rhinovirus CMutation(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)
Find proteins for E5D8F2 (Rhinovirus C)
Go to UniProtKB:  E5D8F2

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP4
D
66Rhinovirus CMutation(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)
Find proteins for E5D8F2 (Rhinovirus C)
Go to UniProtKB:  E5D8F2

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cadherin-related family member 3
U
132Homo sapiensMutation(s): 0 
Gene Names: CDHR3CDH28
Find proteins for Q6ZTQ4 (Homo sapiens)
Go to UniProtKB:  Q6ZTQ4
NIH Common Fund Data Resources
PHAROS  Q6ZTQ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
U
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History 

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2020-04-15
    Changes: Database references