Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (3D View)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

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

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 94.90 kDa 
• Atom Count: 6535 
• Modelled Residue Count: 842 
• Deposited Residue Count: 862 
• Unique protein chains: 4

6DIZ

EV-A71 strain 11316 complexed with tryptophan dendrimer MADAL_0385

• PDB DOI: 10.2210/pdb6DIZ/pdb
• EM Map EMD-7913: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Enterovirus A71
• Mutation(s): No 


• Deposited: 2018-05-24 Released: 2019-04-24 
• Deposition Author(s): Sun, L., Lee, H., Thibaut, H.J., Rivero-Buceta, E., Martinez-Gualda, B., Delang, L., Leyssen, P., Gago, F., San-Felix, A., Hafenstein, S., Mirabelli, C., Neyts, J.
• Funding Organization(s): European Regional Development Fund

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Viral engagement with host (co-)receptors blocked by a novel class of tryptophan dendrimers that targets the 5-fold-axis of the enterovirus-A71 capsid.

Sun, L., Lee, H., Thibaut, H.J., Lanko, K., Rivero-Buceta, E., Bator, C., Martinez-Gualda, B., Dallmeier, K., Delang, L., Leyssen, P., Gago, F., San-Felix, A., Hafenstein, S., Mirabelli, C., Neyts, J.

(2019) PLoS Pathog 15: e1007760-e1007760

• PubMed: 31071193 
• DOI: 10.1371/journal.ppat.1007760
• Primary Citation of Related Structures:  
  6DIZ


• PubMed Abstract: 
  

Enterovirus A71 (EV-A71) is a non-polio neurotropic enterovirus with pandemic potential. There are no antiviral agents approved to prevent or treat EV-A71 infections. We here report on the molecular mechanism by which a novel class of tryptophan dendrimers inhibits (at low nanomolar to high picomolar concentration) EV-A71 replication in vitro. A lead compound in the series (MADAL385) prevents binding and internalization of the virus but does not, unlike classical capsid binders, stabilize the particle. By means of resistance selection, reverse genetics and cryo-EM, we map the binding region of MADAL385 to the 5-fold vertex of the viral capsid and demonstrate that a single molecule binds to each vertex. By interacting with this region, MADAL385 prevents the interaction of the virus with its cellular receptors PSGL1 and heparan sulfate, thereby blocking the attachment of EV-A71 to the host cells.

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Organizational Affiliation: 

KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	297	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for I6W7A3 (Human enterovirus 71) Explore I6W7A3  Go to UniProtKB:  I6W7A3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B	245	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for I6W7A3 (Human enterovirus 71) Explore I6W7A3  Go to UniProtKB:  I6W7A3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C	242	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for I6W7A3 (Human enterovirus 71) Explore I6W7A3  Go to UniProtKB:  I6W7A3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VP4	D	78	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for I6W7A3 (Human enterovirus 71) Explore I6W7A3  Go to UniProtKB:  I6W7A3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPH	E [auth A]	SPHINGOSINE C18 H37 N O2 WWUZIQQURGPMPG-MSOLQXFVSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-24 
• Released Date: 2019-04-24 
Deposition Author(s): Sun, L., Lee, H., Thibaut, H.J., Rivero-Buceta, E., Martinez-Gualda, B., Delang, L., Leyssen, P., Gago, F., San-Felix, A., Hafenstein, S., Mirabelli, C., Neyts, J.

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Funding Organization	Location	Grant Number
European Regional Development Fund		--

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Other