6I2K

Structure of EV71 complexed with its receptor SCARB2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 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

Unexpected mode of engagement between enterovirus 71 and its receptor SCARB2.

Zhou, D.Zhao, Y.Kotecha, A.Fry, E.E.Kelly, J.T.Wang, X.Rao, Z.Rowlands, D.J.Ren, J.Stuart, D.I.

(2019) Nat Microbiol 4: 414-419

  • DOI: 10.1038/s41564-018-0319-z

  • PubMed Abstract: 
  • Enterovirus 71 (EV71) is a common cause of hand, foot and mouth disease-a disease endemic especially in the Asia-Pacific region <sup>1 </sup>. Scavenger receptor class B member 2 (SCARB2) is the major receptor of EV71, as well as several other entero ...

    Enterovirus 71 (EV71) is a common cause of hand, foot and mouth disease-a disease endemic especially in the Asia-Pacific region 1 . Scavenger receptor class B member 2 (SCARB2) is the major receptor of EV71, as well as several other enteroviruses responsible for hand, foot and mouth disease, and plays a key role in cell entry 2 . The isolated structures of EV71 and SCARB2 are known 3-6 , but how they interact to initiate infection is not. Here, we report the EV71-SCARB2 complex structure determined at 3.4 Å resolution using cryo-electron microscopy. This reveals that SCARB2 binds EV71 on the southern rim of the canyon, rather than across the canyon, as predicted 3,7,8 . Helices 152-163 (α5) and 183-193 (α7) of SCARB2 and the viral protein 1 (VP1) GH and VP2 EF loops of EV71 dominate the interaction, suggesting an allosteric mechanism by which receptor binding might facilitate the low-pH uncoating of the virus in the endosome/lysosome. Remarkably, many residues within the binding footprint are not conserved across SCARB2-dependent enteroviruses; however, a conserved proline and glycine seem to be key residues. Thus, although the virus maintains antigenic variability even within the receptor-binding footprint, the identification of binding 'hot spots' may facilitate the design of receptor mimic therapeutics less likely to quickly generate resistance.


    Organizational Affiliation

    Diamond Light Source, Didcot, UK. dave@strubi.ox.ac.uk.,Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. dave@strubi.ox.ac.uk.,Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. ren@strubi.ox.ac.uk.,Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands.,Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China.,The Pirbright Institute, Pirbright, UK.,School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
A
297Human enterovirus 71 (strain 7423/MS/87)Mutation(s): 0 
Find proteins for Q66479 (Human enterovirus 71 (strain 7423/MS/87))
Go to UniProtKB:  Q66479
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
B
254Human enterovirus 71 (strain 7423/MS/87)Mutation(s): 0 
Find proteins for Q66479 (Human enterovirus 71 (strain 7423/MS/87))
Go to UniProtKB:  Q66479
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
C
242Human enterovirus 71 (strain 7423/MS/87)Mutation(s): 0 
Find proteins for Q66479 (Human enterovirus 71 (strain 7423/MS/87))
Go to UniProtKB:  Q66479
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
D
58Human enterovirus 71 (strain 7423/MS/87)Mutation(s): 0 
Find proteins for Q66479 (Human enterovirus 71 (strain 7423/MS/87))
Go to UniProtKB:  Q66479
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Lysosome membrane protein 2
E
416Homo sapiensMutation(s): 0 
Gene Names: SCARB2 (CD36L2, LIMP2, LIMPII)
Find proteins for Q14108 (Homo sapiens)
Go to Gene View: SCARB2
Go to UniProtKB:  Q14108
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
906
Query on 906

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Download CCD File 
A
1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one
C23 H31 N5 O3
SRJKGDFZRYDLKM-WYZSWBMLSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N00065X/1

Revision History 

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-19
    Type: Data collection, Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Database references