PDBsum entry 7jvb

Viral protein

PDB id: 7jvb

Contents

Protein chains

194 a.a.

117 a.a.

Ligands

CAC ×4

PDB id:

7jvb

Name:

Viral protein

Title:

Crystal structure of the sars-cov-2 spike receptor-binding domain (rbd) with nanobody nb20

Structure:

Spike protein s1. Chain: a, b. Synonym: s glycoprotein,e2,peplomer protein,spike glycoprotein. Engineered: yes. Nanobody nb20. Chain: c, d. Engineered: yes

Source:

Severe acute respiratory syndrome coronavirus 2. 2019-ncov, sars-cov-2, covid-19 virus. Organism_taxid: 2697049. Gene: s, 2. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Lama glama. Organism_taxid: 9844.

Resolution:

3.29Å R-factor: 0.283 R-free: 0.322

Authors:

Y.Xiang,Z.Xiao,H.Liu,Z.Sang,D.Schneidman-Duhovny,C.Zhang,Y.Shi

Key ref:

Y.Xiang et al. (2020). Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Science, 370, 1479-1484. PubMed id: 33154108

Date:

20-Aug-20 Release date: 02-Dec-20

Protein chains

P0DTC2  (SPIKE_SARS2) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus 2

Seq: 1273 a.a.

Struc: 194 a.a.

Protein chains

No UniProt id for this chain

Struc: 117 a.a.

Science 370:1479-1484 (2020)

PubMed id: 33154108

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

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

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.