7EY4 | pdb_00007ey4

Local CryoEM of the SARS-CoV-2 S6PV2 in complex with BD-667

• PDB DOI: https://doi.org/10.2210/pdb7EY4/pdb
• EM Map EMD-31377: EMDB EMDataResource

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


• Deposited: 2021-05-29 Released: 2021-09-08 
• Deposition Author(s): Liu, P.L.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.69 Å
• Aggregation State: 3D ARRAY 
• 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 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 224.67 kDa 
• Atom Count: 4,683 
• Modeled Residue Count: 585 
• Deposited Residue Count: 2,027 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-667 L	A [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-667 H	B [auth H]	240	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth R]	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	D [auth N]	287	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.69 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-08 
Deposition Author(s): Liu, P.L.

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release
  
• Version 1.1: 2021-09-15
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2022-02-16
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.4: 2025-07-02
  Changes: Data collection