7EY5 | pdb_00007ey5

Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab

• PDB DOI: https://doi.org/10.2210/pdb7EY5/pdb
• EM Map EMD-31378: EMDB EMDataResource

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


• Deposited: 2021-05-29 Released: 2021-09-08 
• Deposition Author(s): Zhang, Z.Y.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants.

Du, S., Liu, P., Zhang, Z., Xiao, T., Yasimayi, A., Huang, W., Wang, Y., Cao, Y., Xie, X.S., Xiao, J.

(2021) Cell Res 31: 1130-1133

• PubMed: 34433900 
• DOI: https://doi.org/10.1038/s41422-021-00555-0
• Primary Citation Related Structures: 
  7EY0, 7EY4, 7EY5, 7EYA, 7EZV

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Organizational Affiliation: 
• State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China.
School of Life Sciences, Peking University, Beijing, China.
Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.
Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.
Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China. [e-mail].
Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China. [e-mail].
School of Life Sciences, Peking University, Beijing, China. [e-mail].
Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China. [e-mail].
Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China. [e-mail].
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. [e-mail].
State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China. [e-mail].
School of Life Sciences, Peking University, Beijing, China. [e-mail].
Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China. [e-mail].
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 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: 239.99 kDa 
• Atom Count: 5,072 
• Modeled Residue Count: 648 
• Deposited Residue Count: 2,186 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,285	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
BD-821H	B	231	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-821L	C	215	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-771H	D [auth H]	241	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-771L	E [auth L]	214	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-08 
Deposition Author(s): Zhang, Z.Y.

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary