8GPY | pdb_00008gpy

Crystal structure of Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv

• PDB DOI: https://doi.org/10.2210/pdb8GPY/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Trichoplusia
• Mutation(s): Yes 


• Deposited: 2022-08-27 Released: 2023-06-28 
• Deposition Author(s): Gao, Y.X., Song, Z.D., Wang, W.M., Guo, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection.

Guo, Y., Zhang, G., Yang, Q., Xie, X., Lu, Y., Cheng, X., Wang, H., Liang, J., Tang, J., Gao, Y., Shang, H., Dai, J., Shi, Y., Zhou, J., Zhou, J., Guo, H., Yang, H., Qi, J., Liu, L., Ma, S., Zhang, B., Huo, Q., Xie, Y., Wu, J., Dong, F., Zhang, S., Lou, Z., Gao, Y., Song, Z., Wang, W., Sun, Z., Yang, X., Xiong, D., Liu, F., Chen, X., Zhu, P., Wang, X., Cheng, T., Rao, Z.

(2023) Nat Commun 14: 3537-3537

• PubMed: 37322000 
• DOI: https://doi.org/10.1038/s41467-023-39267-x
• Primary Citation Related Structures: 
  7YVE, 7YVF, 7YVG, 7YVH, 7YVI, 7YVJ, 7YVK, 7YVL, 7YVM, 7YVN, 7YVO, 7YVP, 8GOU, 8GPY


• PubMed Abstract: 
  

  The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT ₅₀ values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection.

---

Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China. [e-mail].
State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. [e-mail].
Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China. [e-mail].
Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China. [e-mail].
State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China.
Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China. [e-mail].
State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China.
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China.
Guangzhou Customs District Technology Center, Guangzhou, 510700, China.
Tianjin Haihe Hospital, Jingu Road, Tianjin, 300071, China.
Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China. [e-mail].
CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China. [e-mail].
State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. [e-mail].
Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China. [e-mail].
Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China. [e-mail].
State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. [e-mail].
Tianjin Haihe Hospital, Jingu Road, Tianjin, 300071, China. [e-mail].
State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. [e-mail].
State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China. [e-mail].
Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China. [e-mail].
CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.48 kDa 
• Atom Count: 6,558 
• Modeled Residue Count: 828 
• Deposited Residue Count: 866 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B	201	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 17  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv	C, D [auth E]	232	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.863	α = 90
b = 92.092	β = 92.4
c = 89.27	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Gao, Y.X., Song, Z.D., Wang, W.M., Guo, Y.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870733, 81890990, 81730006, 82022002
Other government	China	2018YFE0200400, 2021YFA1100900, 2021YFA1102800

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 2.0: 2024-03-13
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-10-23
  Changes: Structure summary