8S0M

Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01

• PDB DOI: https://doi.org/10.2210/pdb8S0M/pdb

• Classification: VIRAL PROTEIN/RECEPTOR
• Organism(s): Homo sapiens, Vicugna pacos, Human coronavirus HKU1 (isolate N5)
• Expression System: Drosophila melanogaster, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-02-14 Released: 2024-06-26 
• Deposition Author(s): Duquerroy, S., Fernandez, I., Rey, F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 0.221 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Structural insights into TMPRSS2 maturation and HKU1 binding

Fernandez, I., Saunders, N., Duquerroy, S., Boland, W.H., Arbabian, A., Baquero, E., Lafaye, P., Haouz, A., Buchrieser, J., Schwartz, O., Rey, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 200.45 kDa 
• Atom Count: 12,662 
• Modelled Residue Count: 1,626 
• Deposited Residue Count: 1,794 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2	A [auth B], B [auth E]	395	Homo sapiens	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody A01	C [auth U], F [auth V]	136	Vicugna pacos	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	D [auth A], E [auth D]	366	Human coronavirus HKU1 (isolate N5)	Mutation(s): 0  Gene Names: S, 3
UniProt
Find proteins for Q0ZME7 (Human coronavirus HKU1 (isolate N5)) Explore Q0ZME7  Go to UniProtKB:  Q0ZME7

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth F]	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth B], I [auth A], J [auth A], M [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	K [auth A], L [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 0.221 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.87	α = 90
b = 201.87	β = 90
c = 210.3	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Duquerroy, S., Fernandez, I., Rey, F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release