Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 84.22 kDa 
• Atom Count: 5906 
• Residue Count: 758 
• Unique protein chains: 4

6ZH9

Ternary complex CR3022 H11-H4 and RBD (SARS-CoV-2)

• DOI: 10.2210/pdb6ZH9/pdb

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


• Deposited: 2020-06-21 Released: 2020-09-02 
• Deposition Author(s): Naismith, J.H., Mikolajek, H., Le Bas, A.
• Funding Organization(s): Wellcome Trust, Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.305 
• R-Value Work: 0.261 

Literature

Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2.

Huo, J., Le Bas, A., Ruza, R.R., Duyvesteyn, H.M.E., Mikolajek, H., Malinauskas, T., Tan, T.K., Rijal, P., Dumoux, M., Ward, P.N., Ren, J., Zhou, D., Harrison, P.J., Weckener, M., Clare, D.K., Vogirala, V.K., Radecke, J., Moynie, L., Zhao, Y., Gilbert-Jaramillo, J., Knight, M.L., Tree, J.A., Buttigieg, K.R., Coombes, N., Elmore, M.J., Carroll, M.W., Carrique, L., Shah, P.N.M., James, W., Townsend, A.R., Stuart, D.I., Owens, R.J., Naismith, J.H.

(2020) Nat Struct Mol Biol 27: 846-854

• PubMed: 32661423 
• DOI: 10.1038/s41594-020-0469-6
• Primary Citation of Related Structures:  
  6ZH9


• PubMed Abstract: 
  

The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than influenza. The SARS-CoV-2 receptor binding domain (RBD) of the spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor as a prelude to viral entry into the cell. Using a naive llama single-domain antibody library and PCR-based maturation, we have produced two closely related nanobodies, H11-D4 and H11-H4, that bind RBD (K _D of 39 and 12 nM, respectively) and block its interaction with ACE2. Single-particle cryo-EM revealed that both nanobodies bind to all three RBDs in the spike trimer. Crystal structures of each nanobody-RBD complex revealed how both nanobodies recognize the same epitope, which partly overlaps with the ACE2 binding surface, explaining the blocking of the RBD-ACE2 interaction. Nanobody-Fc fusions showed neutralizing activity against SARS-CoV-2 (4-6 nM for H11-H4, 18 nM for H11-D4) and additive neutralization with the SARS-CoV-1/2 antibody CR3022.

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Organizational Affiliation: 

Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CR3022 heavy	HHH	216	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CR3022 Light chain	LLL	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	EEE	197	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody H11-H4	FFF	134	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.305 
• R-Value Work: 0.261 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.411	α = 90
b = 156.411	β = 90
c = 116.205	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-06-21 
• Released Date: 2020-09-02 
Deposition Author(s): Naismith, J.H., Mikolajek, H., Le Bas, A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	100209/Z/12/Z).
Engineering and Physical Sciences Research Council	United Kingdom	RFI

Revision History 

• Version 1.0: 2020-09-02
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references