9IQP | pdb_00009iqp

Crystal structure of the Wuhan SARS-CoV-2 Spike RBD (319-541) complexed with 1p1B10 nanobody

• PDB DOI: https://doi.org/10.2210/pdb9IQP/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: 2024-07-13 Released: 2025-07-16 
• Deposition Author(s): Sluchanko, N.N., Matyuta, I.O., Dronova, E.A., Favorskaya, I.A., Esmagambetov, I.B., Shcheblyakov, D.V., Logunov, D.Y., Gintsburg, A.L., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.174 (DCC) 

Starting Model: in silico

Literature

Ultra-potent RBM-specific single-domain antibody broadly neutralizes multiple SARS-CoV-2 variants with picomolar activity.

Shcheblyakov, D.V., Favorskaya, I.A., Dolzhikova, I.V., Korobkova, A.I., Alekseeva, I.A., Esmagambetov, I.B., Voronina, O.L., Tukhvatulin, A.I., Zubkova, O.V., Derkaev, A.A., Ryabova, E.I., Iliukhina, A.A., Zorkov, I.D., Grousova, D.M., Reshetnikov, D.A., Ryzhova, N.N., Ermolova, E.I., Kunda, M.S., Matyuta, I.O., Boyko, K.M., Popov, V.O., Logunov, D.Y., Sluchanko, N.N., Gintsburg, A.L.

(2025) Int J Biol Macromol 319: 145386-145386

• PubMed: 40543774 
• DOI: https://doi.org/10.1016/j.ijbiomac.2025.145386
• Primary Citation of Related Structures:  
  9IQP


• PubMed Abstract: 
  

  SARS-CoV-2 infection remains a cause of severe illness in high-risk individuals, with few antiviral agents currently available. The emergence of new SARS-CoV-2 variants accumulating an increasing number of mutations significantly challenges the development of effective therapeutics. We describe broadly neutralizing single-domain antibody 1p1B10 having picomolar activity against both previously circulating SARS-CoV-2 variants, including Wuhan D614G, Alpha, Beta, Gamma, Delta and Omicron BA.1, BA.2, BA.5, and more recent variants - XBB.1, XBB.1.5, XBB.1.9, XBB.1.16, JN.1 and KS.1. We explained this broad activity by solving a high-resolution crystal structure of the S-protein RBD complex with the 1p1B10 antibody. The RBD/1p1B10 interface is unaffected by accumulated mutations and substantially overlaps with the RBD/ACE2 interface. 1p1B10 acts through binding to RBD both in open and closed conformations and blocking SARS-CoV-2 attachment to cells via direct competition with the ACE2 receptor. Therapeutic 1p1B10-Fc administration at a low dose of 1 mg/kg substantially reduced viral load in the lungs of Syrian hamsters after challenge with evolutionary distant SARS-CoV-2 variants and completely protected hACE2 mice against lethal SARS-CoV-2 infection. Overall, the findings make 1p1B10 a promising candidate for etiotropic treatment of COVID-19.

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Organizational Affiliation: 
• Federal State Budget Institution "National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia. Electronic address: [e-mail].
Federal State Budget Institution "National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia. Electronic address: [e-mail].

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

Macromolecule Content 

• Total Structure Weight: 43.24 kDa 
• Atom Count: 2,967 
• Modeled Residue Count: 321 
• Deposited Residue Count: 385 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	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 1p1B10	B	150	Camelus bactrianus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.174 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.33	α = 90
b = 47.05	β = 102.991
c = 60.15	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Sluchanko, N.N., Matyuta, I.O., Dronova, E.A., Favorskaya, I.A., Esmagambetov, I.B., Shcheblyakov, D.V., Logunov, D.Y., Gintsburg, A.L., Popov, V.O., Boyko, K.M.

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Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	075-15-2021-1354

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release