9MWZ | pdb_00009mwz

Cryo-EM Structure of Human Enterovirus D68 USA/IL/14-18952

• PDB DOI: https://doi.org/10.2210/pdb9MWZ/pdb
• EM Map EMD-48705: EMDB EMDataResource

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


• Deposited: 2025-01-17 Released: 2025-03-26 
• Deposition Author(s): Xu, L., Pintilie, G., Varanese, L., Carette, J.E., Chiu, W.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

MFSD6 is an entry receptor for enterovirus D68.

Varanese, L., Xu, L., Peters, C.E., Pintilie, G., Roberts, D.S., Raj, S., Liu, M., Ooi, Y.S., Diep, J., Qiao, W., Richards, C.M., Callaway, J., Bertozzi, C.R., Jabs, S., de Vries, E., van Kuppeveld, F.J.M., Nagamine, C.M., Chiu, W., Carette, J.E.

(2025) Nature 641: 1268-1275

• PubMed: 40132641 
• DOI: https://doi.org/10.1038/s41586-025-08908-0
• Primary Citation of Related Structures:  
  9MWZ, 9MXC


• PubMed Abstract: 
  

  With the near eradication of poliovirus due to global vaccination campaigns, attention has shifted to other enteroviruses that can cause polio-like paralysis syndrome (now termed acute flaccid myelitis (AFM)) ^1-3 . In particular, enterovirus D68 (EV-D68) is believed to be the main driver of epidemic outbreaks of AFM in recent years ⁴ , yet not much is known about EV-D68 host interactions. EV-D68 is a respiratory virus ⁵ but, in rare cases, can spread to the central nervous system to cause severe neuropathogenesis. Here, we used genome-scale CRISPR screens to identify the poorly characterized multipass membrane transporter MFSD6 as a host entry factor for EV-D68. Knockout of MFSD6 expression abrogated EV-D68 infection in cell lines and primary cells corresponding to respiratory and neural cells. MFSD6 localized to the plasma membrane and was required for viral entry into host cells. MFSD6 bound directly to EV-D68 particles via its third extracellular loop (L3). We determined the cryo-EM structure of EV-D68 in complex with L3 at 2.1 Å resolution, revealing the interaction interface. A decoy receptor, engineered by fusing MFSD6(L3) to Fc, blocked EV-D68 infection of human primary lung epithelial cells, and provided near complete protection in a lethal mouse model of EV-D68 infection. Collectively, our results reveal MFSD6 as an entry receptor for EV-D68, and support targeting MFSD6 as a potential mechanism to combat infections by this emerging pathogen with pandemic potential.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Bioengineering, Stanford University, Stanford, CA, USA.
Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
Department of Chemistry, Stanford University, Stanford, CA, USA.
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Virology Group, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany.
Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Department of Bioengineering, Stanford University, Stanford, CA, USA. [e-mail].
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA. [e-mail].
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 89.94 kDa 
• Atom Count: 6,366 
• Modeled Residue Count: 811 
• Deposited Residue Count: 811 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 1	A	297	enterovirus D68	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 A0A097HUV1 (Human enterovirus D68) Explore A0A097HUV1  Go to UniProtKB:  A0A097HUV1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 2	B	237	enterovirus D68	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 A0A191Z5D8 (Human enterovirus D68) Explore A0A191Z5D8  Go to UniProtKB:  A0A191Z5D8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 3	C	247	enterovirus D68	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 A0A1B3ILI7 (Human enterovirus D68) Explore A0A1B3ILI7  Go to UniProtKB:  A0A1B3ILI7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 4	D	30	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42  Go to UniProtKB:  Q68T42

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	ISOLDE

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Xu, L., Pintilie, G., Varanese, L., Carette, J.E., Chiu, W.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE-1656518

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release
  
• Version 1.1: 2025-04-02
  Changes: Data collection, Database references
• Version 1.2: 2025-04-09
  Changes: Data collection, Database references
• Version 1.3: 2025-06-11
  Changes: Data collection, Database references