8ZER

Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody

• PDB DOI: https://doi.org/10.2210/pdb8ZER/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Camelus bactrianus
• Expression System: Cricetulus griseus, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-06 Released: 2024-09-04 
• Deposition Author(s): Sluchanko, N.N., Varfolomeeva, L.A., Shcheblyakov, D.V., Logunov, D.Y., Gintsburg, A.L., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.283 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Starting Models: experimental, in silico

Literature

Structural Basis for Evasion of New SARS-CoV-2 Variants from the Potent Virus-Neutralizing Nanobody Targeting the S-Protein Receptor-Binding Domain

Sluchanko, N.N., Shcheblyakov, D.V., Varfolomeeva, L.A., Favorskaya, I.A., Dolzhikova, I.V., Korobkova, A.I., Alekseeva, I.A., Esmagambetov, I.B., Derkaev, A.A., Prokofiev, V.V., Zorkov, I.D., Logunov, D.Y., Gintsburg, A.L., Popov, V.O., Boyko, K.M.

(2024) Biochemistry Mosc 47 89: 1260-1272

• DOI: https://doi.org/10.1134/S0006297924070083

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 216.77 kDa 
• Atom Count: 12,475 
• Modelled Residue Count: 1,569 
• Deposited Residue Count: 1,905 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth B], C, E, G, I	235	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody P2C5	B [auth A], D, F, H, J	146	Camelus bactrianus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, N	3		N-Glycosylation

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	L, M	2		N-Glycosylation

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	7		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.283 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.483	α = 90
b = 177.458	β = 90
c = 209.861	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Sluchanko, N.N., Varfolomeeva, L.A., Shcheblyakov, D.V., Logunov, D.Y., Gintsburg, A.L., Popov, V.O., Boyko, K.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release