8OWT

SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound

• PDB DOI: https://doi.org/10.2210/pdb8OWT/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Lama glama, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2023-04-28 Released: 2024-05-08 
• Deposition Author(s): Mikolajek, H., Naismith, J.H., Owens, R.J.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 

Literature

Trimeric nanobodies potently neutralize Omicron variants of SARS-CoV-2

Cornish, K.A.S., Mikolajek, H., Naismith, J.H., Owens, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 107.3 kDa 
• Atom Count: 7,194 
• Modelled Residue Count: 893 
• Deposited Residue Count: 956 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody A8	A [auth AAA], D [auth DDD]	132	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth BBB], E [auth EEE]	210	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody H3	C [auth CCC], F [auth FFF]	136	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth BBB], H [auth EEE]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	I [auth EEE]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.609	α = 90
b = 97.197	β = 90
c = 117.583	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Mikolajek, H., Naismith, J.H., Owens, R.J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	223733/Z/21/Z

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release