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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1073/pnas.1921640117
  • Primary Citation of Related Structures:  
    6PPO, 6PSF

  • 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 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

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1279Rhinovirus 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)
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15))
Explore E5D8F2 
Go to UniProtKB:  E5D8F2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5D8F2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3235Rhinovirus 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)
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15))
Explore E5D8F2 
Go to UniProtKB:  E5D8F2
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UniProt GroupE5D8F2
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2265Rhinovirus 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)
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15))
Explore E5D8F2 
Go to UniProtKB:  E5D8F2
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UniProt GroupE5D8F2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP466Rhinovirus 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)
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15))
Explore E5D8F2 
Go to UniProtKB:  E5D8F2
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UniProt GroupE5D8F2
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cadherin-related family member 3E [auth U]132Homo sapiensMutation(s): 0 
Gene Names: CDHR3CDH28
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZTQ4 (Homo sapiens)
Explore Q6ZTQ4 
Go to UniProtKB:  Q6ZTQ4
PHAROS:  Q6ZTQ4
GTEx:  ENSG00000128536 
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UniProt GroupQ6ZTQ4
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONJ3DR
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description