7F3Q

SARS-CoV-2 RBD in complex with A5-10 Fab and A34-2 Fab

• PDB DOI: https://doi.org/10.2210/pdb7F3Q/pdb
• EM Map EMD-31434: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-06-16 Released: 2022-06-22 
• Deposition Author(s): Dou, Y., Wang, X., Liu, P., Lu, B., Wang, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Development of neutralizing antibodies against SARS-CoV-2, using a high-throughput single-B-cell cloning method.

Dou, Y., Xu, K., Deng, Y.Q., Jia, Z., Lan, J., Xu, X., Zhang, G., Cao, T., Liu, P., Wang, X., Wang, X., Xu, L., Du, P., Qin, C.F., Liu, H., Li, Y., Wu, G., Wang, K., Lu, B.

(2023) Antib Ther 6: 76-86

• PubMed: 37077472 
• DOI: https://doi.org/10.1093/abt/tbad002
• Primary Citation of Related Structures:  
  7F3Q


• PubMed Abstract: 
  

  Rapid and efficient strategies are needed to discover neutralizing antibodies (nAbs) from B cells derived from virus-infected patients.

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Organizational Affiliation: 

School of Pharmaceutical Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 234.01 kDa 
• Atom Count: 8,003 
• Modelled Residue Count: 1,050 
• Deposited Residue Count: 2,138 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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
Heavy chain of A34-2 Fab	B [auth H]	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of A34-2 Fab	C [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of A5-10 Fab	D [auth C]	227	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of A5-10 Fab	E [auth B]	205	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES (Subject of Investigation/LOI)	G [auth H]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Dou, Y., Wang, X., Liu, P., Lu, B., Wang, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references