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 8Y89

Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 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

TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry.

Wang, H.Liu, X.Zhang, X.Zhao, Z.Lu, Y.Pu, D.Zhang, Z.Chen, J.Wang, Y.Li, M.Dong, X.Duan, Y.He, Y.Mao, Q.Guo, H.Sun, H.Zhou, Y.Yang, Q.Gao, Y.Yang, X.Cao, H.Guddat, L.Sun, L.Rao, Z.Yang, H.

(2024) Cell 187: 4261

  • DOI: https://doi.org/10.1016/j.cell.2024.06.016
  • Primary Citation of Related Structures:  
    8Y7X, 8Y7Y, 8Y87, 8Y88, 8Y89, 8Y8A, 8Y8B, 8Y8C, 8Y8D, 8Y8E, 8Y8F, 8Y8G, 8Y8H, 8Y8I, 8Y8J

  • PubMed Abstract: 

    The entry of coronaviruses is initiated by spike recognition of host cellular receptors, involving proteinaceous and/or glycan receptors. Recently, TMPRSS2 was identified as the proteinaceous receptor for HCoV-HKU1 alongside sialoglycan as a glycan receptor. However, the underlying mechanisms for viral entry remain unknown. Here, we investigated the HCoV-HKU1C spike in the inactive, glycan-activated, and functionally anchored states, revealing that sialoglycan binding induces a conformational change of the NTD and promotes the neighboring RBD of the spike to open for TMPRSS2 recognition, exhibiting a synergistic mechanism for the entry of HCoV-HKU1. The RBD of HCoV-HKU1 features an insertion subdomain that recognizes TMPRSS2 through three previously undiscovered interfaces. Furthermore, structural investigation of HCoV-HKU1A in combination with mutagenesis and binding assays confirms a conserved receptor recognition pattern adopted by HCoV-HKU1. These studies advance our understanding of the complex viral-host interactions during entry, laying the groundwork for developing new therapeutics against coronavirus-associated diseases.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA,
B [auth C],
C [auth B]
1,263Human coronavirus HKU1 (isolate N5)Mutation(s): 10 
Gene Names: S3
UniProt
Find proteins for Q0ZME7 (Human coronavirus HKU1 (isolate N5))
Explore Q0ZME7 
Go to UniProtKB:  Q0ZME7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ZME7
Glycosylation
Glycosylation Sites: 9
Sequence AnnotationsExpand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protease serine 2D [auth T],
E [auth G]
383Homo sapiensMutation(s): 5 
Gene Names: TMPRSS2PRSS10
EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens)
Explore O15393 
Go to UniProtKB:  O15393
PHAROS:  O15393
GTEx:  ENSG00000184012 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15393
Sequence AnnotationsExpand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F [auth D],
G [auth E],
H [auth F],
I [auth H],
J [auth I],
F [auth D],
G [auth E],
H [auth F],
I [auth H],
J [auth I],
K [auth J],
L [auth K],
M [auth L],
N [auth M],
O [auth N]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseP [auth O]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
Q [auth A]
R [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China92169109

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary