8TZU

OC43 S1b domain in complex with WNb 293 and WNb 317

• PDB DOI: https://doi.org/10.2210/pdb8TZU/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human coronavirus OC43, Vicugna pacos
• Expression System: Homo sapiens, Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2023-08-27 Released: 2024-05-01 
• Deposition Author(s): Pymm, P., Feng, J., Tham, W.H.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.266 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

OC43 S1b domain in complex with WNb 293 and WNb 317

Pymm, P., Feng, J., Tham, W.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 160.34 kDa 
• Atom Count: 10,985 
• Modelled Residue Count: 1,405 
• Deposited Residue Count: 1,444 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B, F	275	Human coronavirus OC43	Mutation(s): 0  Gene Names: S, 3
UniProt
Find proteins for P36334 (Human coronavirus OC43) Explore P36334  Go to UniProtKB:  P36334

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WNb 317	C, G, H	121	Vicugna pacos	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
WNb 293	D, E	128	Vicugna pacos	Mutation(s): 0

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	I [auth L], J [auth N], M [auth K]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth I]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth J]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	N [auth A], O [auth A], P [auth C], Q [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.266 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.914	α = 90
b = 150.61	β = 90
c = 155.111	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Pymm, P., Feng, J., Tham, W.H.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	2021267

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release