9IZN | pdb_00009izn

Crystal structure of HKU1A RBD bound to TMPRSS2

• PDB DOI: https://doi.org/10.2210/pdb9IZN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Human coronavirus HKU1 (isolate N1)
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): Yes 


• Deposited: 2024-08-01 Released: 2024-10-23 
• Deposition Author(s): Wang, W., Xu, Y., Zhang, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Models: experimental

Literature

High-resolution crystal structure of human coronavirus HKU1 receptor binding domain bound to TMPRSS2 receptor

Wang, W., Guan, J., Ren, M., Li, Z., Ji, W., Chen, R., Xu, Y., Zhang, S.

(2024) Hlife 

• DOI: https://doi.org/10.1016/j.hlife.2024.09.005

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 86.45 kDa 
• Atom Count: 5,771 
• Modelled Residue Count: 696 
• Deposited Residue Count: 771 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2	A [auth B]	392	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
Spike protein S1	B [auth A]	379	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
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.324	α = 90
b = 78.358	β = 90
c = 257.364	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Wang, W., Xu, Y., Zhang, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32170158
National Natural Science Foundation of China (NSFC)	China	32000659

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release