7KN5

Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U

• PDB DOI:  https://doi.org/10.2210/pdb7KN5/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-04 Released: 2021-01-20 
• Deposition Author(s): Liu, H., Yuan, M., Zhu, X., Wu, N.C., Wilson, I.A.
• Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.213 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.

Koenig, P.A., Das, H., Liu, H., Kummerer, B.M., Gohr, F.N., Jenster, L.M., Schiffelers, L.D.J., Tesfamariam, Y.M., Uchima, M., Wuerth, J.D., Gatterdam, K., Ruetalo, N., Christensen, M.H., Fandrey, C.I., Normann, S., Todtmann, J.M.P., Pritzl, S., Hanke, L., Boos, J., Yuan, M., Zhu, X., Schmid-Burgk, J.L., Kato, H., Schindler, M., Wilson, I.A., Geyer, M., Ludwig, K.U., Hallberg, B.M., Wu, N.C., Schmidt, F.I.

(2021) Science 371

• PubMed: 33436526 
• DOI: https://doi.org/10.1126/science.abe6230
• Primary Citation of Related Structures:  
  7B14, 7B17, 7B18, 7KN5, 7KN6, 7KN7, 7KSG


• PubMed Abstract: 
  

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost advantages over conventional antibodies. In this study, we generated four neutralizing nanobodies that target the receptor binding domain of the SARS-CoV-2 spike protein. We used x-ray crystallography and cryo-electron microscopy to define two distinct binding epitopes. On the basis of these structures, we engineered multivalent nanobodies with more than 100 times the neutralizing activity of monovalent nanobodies. Biparatopic nanobody fusions suppressed the emergence of escape mutants. Several nanobody constructs neutralized through receptor binding competition, whereas other monovalent and biparatopic nanobodies triggered aberrant activation of the spike fusion machinery. These premature conformational changes in the spike protein forestalled productive fusion and rendered the virions noninfectious.

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Organizational Affiliation: 

Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 108.77 kDa 
• Atom Count: 7,282 
• Modelled Residue Count: 892 
• Deposited Residue Count: 972 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B	231	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH E	C, D	129	Vicugna pacos	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH U	E, F	126	Vicugna pacos	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO (Subject of Investigation/LOI)	H [auth A], I [auth A], J [auth A], L [auth C], M [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.213 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.525	α = 90
b = 91.943	β = 91.147
c = 84.998	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Liu, H., Yuan, M., Zhu, X., Wu, N.C., Wilson, I.A.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI139445

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references
• Version 1.2: 2021-02-24
  Changes: Database references