7E9P

Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(state2, local refinement of the RBD and 35B5 Fab)

• PDB DOI: https://doi.org/10.2210/pdb7E9P/pdb
• EM Map EMD-31035: EMDB EMDataResource

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


• Deposited: 2021-03-04 Released: 2022-03-23 
• Deposition Author(s): Wang, X.F., Zhu, Y.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A potent human monoclonal antibody with pan-neutralizing activities directly dislocates S trimer of SARS-CoV-2 through binding both up and down forms of RBD

Wang, X., Hu, A., Chen, X., Zhang, Y., Yu, F., Yue, S., Li, A., Zhang, J., Pan, Z., Yang, Y., Lin, Y., Gao, L., Zhou, J., Zhao, J., Li, F., Shi, Y., Huang, F., Yang, X., Peng, Y., Tu, L., Zhang, H., Zheng, H., He, J., Zhang, H., Xu, L., Huang, Q., Zhu, Y., Deng, K., Ye, L.

(2022) Signal Transduct Target Ther 7: 114

• DOI: https://doi.org/10.1038/s41392-022-00954-8

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 191.69 kDa 
• Atom Count: 4,898 
• Modelled Residue Count: 639 
• Deposited Residue Count: 1,744 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B]	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of 35B5 Fab	B [auth L]	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of 35B5 Fab	C [auth H]	237	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [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: 3.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.15

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Wang, X.F., Zhu, Y.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81530068
National Natural Science Foundation of China (NSFC)	China	81501717

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2022-09-21
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary