7X1M image
Deposition Date 2022-02-24
Release Date 2022-07-06
Last Version Date 2025-07-02
Entry Detail
PDB ID:
7X1M
Title:
The complex structure of Omicron BA.1 RBD with BD604, S309,and S304
Biological Source:
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.74 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:S309 Fab heavy chain
Chain IDs:A
Chain Length:230
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:S309 Fab light chain
Chain IDs:B
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BD-604 Fab heavy chain
Chain IDs:C
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BD-604 Fab light chain
Chain IDs:D
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:S304 Fab haavy chain
Chain IDs:E (auth: H)
Chain Length:223
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:S304 Fab light chain
Chain IDs:F (auth: L)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:G (auth: M)
Chain Length:209
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Ligand Molecules
Primary Citation
Atlas of currently available human neutralizing antibodies against SARS-CoV-2 and escape by Omicron sub-variants BA.1/BA.1.1/BA.2/BA.3.
Immunity 55 1501 1514.e3 (2022)
PMID: 35777362 DOI: 10.1016/j.immuni.2022.06.005

Abstact

SARS-CoV-2 Omicron variant has presented significant challenges to current antibodies and vaccines. Herein, we systematically compared the efficacy of 50 human monoclonal antibodies (mAbs), covering the seven identified epitope classes of the SARS-CoV-2 RBD, against Omicron sub-variants BA.1, BA.1.1, BA.2, and BA.3. Binding and pseudovirus-based neutralizing assays revealed that 37 of the 50 mAbs lost neutralizing activities, whereas the others displayed variably decreased activities against the four Omicron sub-variants. BA.2 was found to be more sensitive to RBD-5 antibodies than the other sub-variants. Furthermore, a quaternary complex structure of BA.1 RBD with three mAbs showing different neutralizing potencies against Omicron provided a basis for understanding the immune evasion of Omicron sub-variants and revealed the lack of G446S mutation accounting for the sensitivity of BA.2 to RBD-5 mAbs. Our results may guide the application of the available mAbs and facilitate the development of universal therapeutic antibodies and vaccines against COVID-19.

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Primary Citation of related structures
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