7KM5 | pdb_00007km5

Crystal structure of SARS-CoV-2 RBD complexed with Nanosota-1

PDB DOI: https://doi.org/10.2210/pdb7KM5/pdb

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

Deposited: 2020-11-02 Released: 2021-08-04
Deposition Author(s): Ye, G., Shi, K., Aihara, H., Li, F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free:
0.294 (Depositor), 0.301 (DCC)
R-Value Work:
0.247 (Depositor), 0.255 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The development of Nanosota - 1 as anti-SARS-CoV-2 nanobody drug candidates.

Ye, G., Gallant, J., Zheng, J., Massey, C., Shi, K., Tai, W., Odle, A., Vickers, M., Shang, J., Wan, Y., Du, L., Aihara, H., Perlman, S., LeBeau, A., Li, F.

(2021) Elife 10

PubMed: 34338634 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.64815
Primary Citation Related Structures:
7KM5

PubMed Abstract:
Combating the COVID-19 pandemic requires potent and low-cost therapeutics. We identified a series of single-domain antibodies (i.e., nanobody), Nanosota-1 , from a camelid nanobody phage display library. Structural data showed that Nanosota-1 bound to the oft-hidden receptor-binding domain (RBD) of SARS-CoV-2 spike protein, blocking viral receptor angiotensin-converting enzyme 2 (ACE2). The lead drug candidate possessing an Fc tag ( Nanosota-1C-Fc ) bound to SARS-CoV-2 RBD ~3000 times more tightly than ACE2 did and inhibited SARS-CoV-2 pseudovirus ~160 times more efficiently than ACE2 did. Administered at a single dose, Nanosota-1C-Fc demonstrated preventive and therapeutic efficacy against live SARS-CoV-2 infection in both hamster and mouse models. Unlike conventional antibodies, Nanosota-1C-Fc was produced at high yields in bacteria and had exceptional thermostability. Pharmacokinetic analysis of Nanosota-1C-F c documented an excellent in vivo stability and a high tissue bioavailability. As effective and inexpensive drug candidates, Nanosota-1 may contribute to the battle against COVID-19.

Organizational Affiliation

Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, United States.

Macromolecule Content

Total Structure Weight: 79.09 kDa
Atom Count: 4,889
Modeled Residue Count: 620
Deposited Residue Count: 698
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B	225	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody	C, D	124	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free: 0.294 (Depositor), 0.301 (DCC)
R-Value Work: 0.247 (Depositor), 0.255 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.849	α = 90
b = 60.849	β = 90
c = 410.701	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01AI089728
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01AI089728
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047