7UHC

SARS-CoV-2 spike in complex with AHB2-2GS-SB175


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice.

Hunt, A.C.Case, J.B.Park, Y.J.Cao, L.Wu, K.Walls, A.C.Liu, Z.Bowen, J.E.Yeh, H.W.Saini, S.Helms, L.Zhao, Y.T.Hsiang, T.Y.Starr, T.N.Goreshnik, I.Kozodoy, L.Carter, L.Ravichandran, R.Green, L.B.Matochko, W.L.Thomson, C.A.Vogeli, B.Kruger, A.VanBlargan, L.A.Chen, R.E.Ying, B.Bailey, A.L.Kafai, N.M.Boyken, S.E.Ljubetic, A.Edman, N.Ueda, G.Chow, C.M.Johnson, M.Addetia, A.Navarro, M.J.Panpradist, N.Gale Jr., M.Freedman, B.S.Bloom, J.D.Ruohola-Baker, H.Whelan, S.P.J.Stewart, L.Diamond, M.S.Veesler, D.Jewett, M.C.Baker, D.

(2022) Sci Transl Med 14: eabn1252-eabn1252

  • DOI: https://doi.org/10.1126/scitranslmed.abn1252
  • Primary Citation of Related Structures:  
    7UHB, 7UHC

  • PubMed Abstract: 

    New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.


  • Organizational Affiliation

    Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA,
C [auth B],
E [auth D]
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 9 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 16Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Multivalent miniprotein inhibitor AHB2-2GS-SB175B [auth K],
D [auth C],
F [auth E]
148synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G [auth F],
H [auth G],
I [auth H],
J [auth I],
K [auth J],
G [auth F],
H [auth G],
I [auth H],
J [auth I],
K [auth J],
L,
M,
N,
O,
P,
Q,
R
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth D]
BA [auth A]
BB [auth D]
CA [auth A]
AA [auth A],
AB [auth D],
BA [auth A],
BB [auth D],
CA [auth A],
DA [auth A],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
OA [auth B],
PA [auth B],
QA [auth D],
RA [auth D],
S [auth A],
SA [auth D],
T [auth A],
TA [auth D],
U [auth A],
UA [auth D],
V [auth A],
VA [auth D],
W [auth A],
WA [auth D],
X [auth A],
XA [auth D],
Y [auth A],
YA [auth D],
Z [auth A],
ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesSSGCID

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Other