8J1V

Cryo-EM structure of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 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 lung-selective delivery of mRNA encoding broadly neutralizing antibody against SARS-CoV-2 infection.

Tai, W.Yang, K.Liu, Y.Li, R.Feng, S.Chai, B.Zhuang, X.Qi, S.Shi, H.Liu, Z.Lei, J.Ma, E.Wang, W.Tian, C.Le, T.Wang, J.Chen, Y.Tian, M.Xiang, Y.Yu, G.Cheng, G.

(2023) Nat Commun 14: 8042-8042

  • DOI: https://doi.org/10.1038/s41467-023-43798-8
  • Primary Citation of Related Structures:  
    8J1T, 8J1V

  • PubMed Abstract: 

    The respiratory system, especially the lung, is the key site of pathological injury induced by SARS-CoV-2 infection. Given the low feasibility of targeted delivery of antibodies into the lungs by intravenous administration and the short half-life period of antibodies in the lungs by intranasal or aerosolized immunization, mRNA encoding broadly neutralizing antibodies with lung-targeting capability can perfectly provide high-titer antibodies in lungs to prevent the SARS-CoV-2 infection. Here, we firstly identify a human monoclonal antibody, 8-9D, with broad neutralizing potency against SARS-CoV-2 variants. The neutralization mechanism of this antibody is explained by the structural characteristics of 8-9D Fabs in complex with the Omicron BA.5 spike. In addition, we evaluate the efficacy of 8-9D using a safe and robust mRNA delivery platform and compare the performance of 8-9D when its mRNA is and is not selectively delivered to the lungs. The lung-selective delivery of the 8-9D mRNA enables the expression of neutralizing antibodies in the lungs which blocks the invasion of the virus, thus effectively protecting female K18-hACE2 transgenic mice from challenge with the Beta or Omicron BA.1 variant. Our work underscores the potential application of lung-selective mRNA antibodies in the prevention and treatment of infections caused by circulating SARS-CoV-2 variants.


  • Organizational Affiliation

    New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S2'A,
D [auth B],
G [auth E]
1,115Severe acute respiratory syndrome coronavirus 2Mutation(s): 39 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
8-9D heavy chainB [auth H],
E [auth C],
H [auth F]
115Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
8-9D light chainC [auth K],
F [auth D],
I [auth G]
108Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth B],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth E],
HA [auth E],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references