7TYZ

Cryo-EM structure of SARS-CoV-2 spike in complex with FSR22, an anti-SARS-CoV-2 DARPin

PDB DOI: https://doi.org/10.2210/pdb7TYZ/pdb
EM Map EMD-26200: EMDB EMDataResource

Classification: VIRAL PROTEIN/ANTIVIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Escherichia phage EcSzw-2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-02-15 Released: 2022-12-07
Deposition Author(s): Kwon, Y.D., Gorman, J., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.51 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A potent and broad neutralization of SARS-CoV-2 variants of concern by DARPins.

Chonira, V., Kwon, Y.D., Gorman, J., Case, J.B., Ku, Z., Simeon, R., Casner, R.G., Harris, D.R., Olia, A.S., Stephens, T., Shapiro, L., Bender, M.F., Boyd, H., Teng, I.T., Tsybovsky, Y., Krammer, F., Zhang, N., Diamond, M.S., Kwong, P.D., An, Z., Chen, Z.

(2023) Nat Chem Biol 19: 284-291

PubMed: 36411391 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41589-022-01193-2
Primary Citation of Related Structures:
7TYZ, 7TZ0, 8DW2, 8DW3

PubMed Abstract:
We report the engineering and selection of two synthetic proteins-FSR16m and FSR22-for the possible treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon. Despite selection by a spike protein from a now historical SARS-CoV-2 strain, FSR16m and FSR22 exhibit broad-spectrum neutralization of SARS-CoV-2 strains, inhibiting authentic B.1.351, B.1.617.2 and BA.1.1 viruses, with respective IC ₅₀ values of 3.4, 2.2 and 7.4 ng ml ^-1 for FSR16m. Cryo-EM structures revealed that these DARPins recognize a region of the receptor-binding domain (residues 456, 475, 486, 487 and 489) overlapping a critical portion of the angiotensin-converting enzyme 2 (ACE2)-binding surface. K18-hACE2 transgenic mice inoculated with B.1.617.2 and receiving intranasally administered FSR16m showed less weight loss and 10-100-fold lower viral burden in upper and lower respiratory tracts. The strong and broad neutralization potency makes FSR16m and FSR22 promising candidates for the prevention and treatment of infection by SARS-CoV-2.

Organizational Affiliation

Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA.

Macromolecule Content

Total Structure Weight: 499.78 kDa
Atom Count: 29,736
Modelled Residue Count: 3,711
Deposited Residue Count: 4,416
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, C, E	1,247	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin FSR22	B, D, F	225	Escherichia phage EcSzw-2	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, R, S	4	N/A	N-Glycosylation	Interactions Focus chain G Focus chain R Focus chain S Interactions & Density Focus chain G Focus chain R Focus chain S
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, K, L, M, P H, K, L, M, P, Q, T, W, X	2	N/A	N-Glycosylation	Interactions Focus chain H Focus chain K Focus chain L Focus chain M Focus chain P Focus chain Q Focus chain T Focus chain W Focus chain X Interactions & Density Focus chain H Focus chain K Focus chain L Focus chain M Focus chain P Focus chain Q Focus chain T Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J, N, O, U I, J, N, O, U, V	3	N/A	N-Glycosylation	Interactions Focus chain I Focus chain J Focus chain N Focus chain O Focus chain U Focus chain V Interactions & Density Focus chain I Focus chain J Focus chain N Focus chain O Focus chain U Focus chain V
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain KA [auth E] SDF format, chain PA [auth E] SDF format, chain Z [auth A] SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain Y [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain Y [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth C] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth E], LA [auth E], MA [auth E], NA [auth E], OA [auth E], PA [auth E], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain Y [auth A] Focus chain Z [auth A]