6AJ3

The structure of Enterovirus D68 procapsid

  • Classification: VIRUS
  • Organism(s): Enterovirus D68
  • Mutation(s): No 

  • Deposited: 2018-08-26 Released: 2018-11-07 
  • Deposition Author(s): Zheng, Q.B., Zhu, R., Xu, L.F., He, M.Z., Yan, X.D., Cheng, T., Li, S.W.
  • Funding Organization(s): National Natural Science Foundation of China, National Institutes of Health/National Institute of General Medical Sciences, National Institutes of Health/National Institute of Dental and Craniofacial Research, National Institutes of Health/National Institute Of Allergy and Infectious Diseases, National Institutes of Health/National Center for Research Resources, National Science Foundation (United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization

Zheng, Q., Zhu, R., Xu, L., He, M., Yan, X., Liu, D., Yin, Z., Wu, Y., Li, Y., Yang, L., Hou, W., Li, S., Li, Z., Chen, Z., Li, Z., Yu, H., Gu, Y., Zhang, J., Baker, T.S., Zhou, Z.H., Graham, B.S., Cheng, T., Li, S., Xia, N.

(2019) Nat Microbiol 4: 124-133

  • DOI: 10.1038/s41564-018-0275-7
  • Primary Citation of Related Structures:  
    6AJ7, 6AJ9, 6AJ0, 6AJ2, 6AJ3

  • PubMed Abstract: 

    • Enterovirus D68 (EV-D68) undergoes structural transformation between mature, cell-entry intermediate (A-particle) and empty forms throughout its life cycle. Structural information for the various forms and antibody-bound capsids will facilitate the devel ...

    Enterovirus D68 (EV-D68) undergoes structural transformation between mature, cell-entry intermediate (A-particle) and empty forms throughout its life cycle. Structural information for the various forms and antibody-bound capsids will facilitate the development of effective vaccines and therapeutics against EV-D68 infection, which causes childhood respiratory and paralytic diseases worldwide. Here, we report the structures of three EV-D68 capsid states representing the virus at major phases. We further describe two original monoclonal antibodies (15C5 and 11G1) with distinct structurally defined mechanisms for virus neutralization. 15C5 and 11G1 engage the capsid loci at icosahedral three-fold and five-fold axes, respectively. To block viral attachment, 15C5 binds three forms of capsids, and triggers mature virions to transform into A-particles, mimicking engagement by the functional receptor ICAM-5, whereas 11G1 exclusively recognizes the A-particle. Our data provide a structural and molecular explanation for the transition of picornavirus capsid conformations and demonstrate distinct mechanisms for antibody-mediated neutralization.

    Organizational Affiliation: 

    State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, School of Public Health, Xiamen University, Xiamen, China. nsxia@xmu.edu.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1 A295Enterovirus D68Mutation(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 A0A097F8Q2 (Human enterovirus D68)
Explore A0A097F8Q2 
Go to UniProtKB:  A0A097F8Q2
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP2 B248Enterovirus D68Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for A0A097F8Q2 (Human enterovirus D68)
Explore A0A097F8Q2 
Go to UniProtKB:  A0A097F8Q2
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP3 C247Enterovirus D68Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for A0A097F8Q2 (Human enterovirus D68)
Explore A0A097F8Q2 
Go to UniProtKB:  A0A097F8Q2
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81401669
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR37-GM33050
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071940
National Institutes of Health/National Institute of General Medical SciencesUnited States1U24GM116792
National Institutes of Health/National Institute of Dental and Craniofacial ResearchUnited StatesDE025567
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI094386
National Institutes of Health/National Center for Research ResourcesUnited States1S10RR23057
National Science Foundation (United States)United StatesDBI-1338135
National Science Foundation (United States)United StatesDMR-1548924
National Science Foundation (United States)United StatesDBI-1338135
National Science Foundation (United States)United StatesDMR-1548924

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-26
    Changes: Data collection, Database references