6ZH9 | pdb_00006zh9

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

• PDB DOI: https://doi.org/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 (Depositor), 0.313 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.265 (DCC) 

Starting Model: experimental

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: https://doi.org/10.1038/s41594-020-0469-6
• Primary Citation 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: 
• Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK.
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK.
Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
Centre for Translational Immunology, Chinse Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
National Infection Service, Public Health England, Porton Down, Salisbury, UK.
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK. [e-mail].
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK. [e-mail].
Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK. [e-mail].
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK. [e-mail].
Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK. [e-mail].
Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK. [e-mail].

Biological Assembly 1  

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: 5,906 
• Modeled Residue Count: 758 
• Deposited Residue Count: 766 
• Unique protein chains: 4

Macromolecules

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

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth EEE]	197	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody H11-H4	D [auth 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 (Depositor), 0.313 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.265 (DCC) 

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

• 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
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary