7U6R

Cryo-EM structure of PDF-2180 Spike glycoprotein

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 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

Close relatives of MERS-CoV in bats use ACE2 as their functional receptors.

Xiong, Q., Cao, L., Ma, C., Tortorici, M.A., Liu, C., Si, J., Liu, P., Gu, M., Walls, A.C., Wang, C., Shi, L., Tong, F., Huang, M., Li, J., Zhao, C., Shen, C., Chen, Y., Zhao, H., Lan, K., Corti, D., Veesler, D., Wang, X., Yan, H.

(2022) Nature 612: 748-757

  • DOI: 10.1038/s41586-022-05513-3
  • Primary Citation of Related Structures:  
    7U6R, 7WPO, 7WPZ

  • PubMed Abstract: 

    • Middle East respiratory syndrome coronavirus (MERS-CoV) and several bat coronaviruses use dipeptidyl peptidase-4 (DPP4) as an entry receptor 1-4 . However, the receptor for NeoCoV-the closest known MERS-CoV relative found in bats-remains unclear 5 ...

    Middle East respiratory syndrome coronavirus (MERS-CoV) and several bat coronaviruses use dipeptidyl peptidase-4 (DPP4) as an entry receptor 1-4 . However, the receptor for NeoCoV-the closest known MERS-CoV relative found in bats-remains unclear 5 . Here, using a pseudotype virus entry assay, we found that NeoCoV and its close relative, PDF-2180, can efficiently bind to and use specific bat angiotensin-converting enzyme 2 (ACE2) orthologues and, less favourably, human ACE2 as entry receptors through their receptor-binding domains (RBDs) on the spike (S) proteins. Cryo-electron microscopy analysis revealed an RBD-ACE2 binding interface involving protein-glycan interactions, distinct from those of other known ACE2-using coronaviruses. We identified residues 337-342 of human ACE2 as a molecular determinant restricting NeoCoV entry, whereas a NeoCoV S pseudotyped virus containing a T510F RBD mutation efficiently entered cells expressing human ACE2. Although polyclonal SARS-CoV-2 antibodies or MERS-CoV RBD-specific nanobodies did not cross-neutralize NeoCoV or PDF-2180, an ACE2-specific antibody and two broadly neutralizing betacoronavirus antibodies efficiently inhibited these two pseudotyped viruses. We describe MERS-CoV-related viruses that use ACE2 as an entry receptor, underscoring a promiscuity of receptor use and a potential zoonotic threat.

    Organizational Affiliation: 

    State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China. huanyan@whu.edu.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PDF-2180 Spike glycoproteinA, B, C1,337Bat coronavirusMutation(s): 0 
Gene Names: S
UniProt
Find proteins for A0A1W6ASU7 (Bat coronavirus)
Explore A0A1W6ASU7 
Go to UniProtKB:  A0A1W6ASU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W6ASU7
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, G, H, I
D, E, F, G, H, I
2N/AN-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
S [auth A],
SA [auth C],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references
  • Version 1.2: 2023-01-04
    Changes: Database references