8VGT

Structure of the HKU1 RBD bound to the human TMPRSS2 receptor

• PDB DOI: https://doi.org/10.2210/pdb8VGT/pdb
• EM Map EMD-43224: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human coronavirus HKU1 (isolate N1), Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-12-27 Released: 2024-03-06 
• Deposition Author(s): Park, Y.J., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Human coronavirus HKU1 recognition of the TMPRSS2 host receptor

Park, Y.J., Veesler, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 84.64 kDa 
• Atom Count: 4,714 
• Modelled Residue Count: 629 
• Deposited Residue Count: 754 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	338	Human coronavirus HKU1 (isolate N1)	Mutation(s): 0  Gene Names: S, 3
UniProt
Find proteins for Q5MQD0 (Human coronavirus HKU1 (isolate N1)) Explore Q5MQD0  Go to UniProtKB:  Q5MQD0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2	B	416	Homo sapiens	Mutation(s): 7  Gene Names: TMPRSS2, PRSS10 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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Park, Y.J., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158186

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release