7JVB | pdb_00007jvb

Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20

• PDB DOI: https://doi.org/10.2210/pdb7JVB/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-08-20 Released: 2020-12-02 
• Deposition Author(s): Xiang, Y., Xiao, Z., Liu, H., Sang, Z., Schneidman-Duhovny, D., Zhang, C., Shi, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 
  0.322 (Depositor), 0.311 (DCC) 
• R-Value Work: 
  0.281 (Depositor), 0.284 (DCC) 
• R-Value Observed: 
  0.283 (Depositor) 

Starting Model: experimental

Literature

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2.

Xiang, Y., Nambulli, S., Xiao, Z., Liu, H., Sang, Z., Duprex, W.P., Schneidman-Duhovny, D., Zhang, C., Shi, Y.

(2020) Science 370: 1479-1484

• PubMed: 33154108 
• DOI: https://doi.org/10.1126/science.abe4747
• Primary Citation Related Structures: 
  7JVB


• PubMed Abstract: 
  

  Cost-effective, efficacious therapeutics are urgently needed to combat the COVID-19 pandemic. In this study, we used camelid immunization and proteomics to identify a large repertoire of highly potent neutralizing nanobodies (Nbs) to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor binding domain (RBD). We discovered Nbs with picomolar to femtomolar affinities that inhibit viral infection at concentrations below the nanograms-per-milliliter level, and we determined a structure of one of the most potent Nbs in complex with the RBD. Structural proteomics and integrative modeling revealed multiple distinct and nonoverlapping epitopes and indicated an array of potential neutralization mechanisms. We bioengineered multivalent Nb constructs that achieved ultrahigh neutralization potency (half-maximal inhibitory concentration as low as 0.058 ng/ml) and may prevent mutational escape. These thermostable Nbs can be rapidly produced in bulk from microbes and resist lyophilization and aerosolization.

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Organizational Affiliation: 
• Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.
Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA.
Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA.
School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. [e-mail] [e-mail] [e-mail].
Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA. [e-mail] [e-mail] [e-mail].
Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 76.01 kDa 
• Atom Count: 4,748 
• Modeled Residue Count: 621 
• Deposited Residue Count: 682 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, C [auth B]	224	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
Nanobody Nb20	B [auth C], D	117	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	E [auth A], F [auth C], G [auth B], H [auth D]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free:  0.322 (Depositor), 0.311 (DCC) 
• R-Value Work:  0.281 (Depositor), 0.284 (DCC) 
• R-Value Observed: 0.283 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.716	α = 90
b = 70.716	β = 90
c = 435.037	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
JBluIce-EPICS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Xiang, Y., Xiao, Z., Liu, H., Sang, Z., Schneidman-Duhovny, D., Zhang, C., Shi, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM128641

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Database references
• Version 1.2: 2021-01-27
  Changes: Structure summary
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary