7E5S | pdb_00007e5s

SARS-CoV-2 S trimer with four-antibody cocktail complex

• PDB DOI: https://doi.org/10.2210/pdb7E5S/pdb
• EM Map EMD-30994: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Mammalian expression vector BsrGI-MCS-pcDNA3.1
• Mutation(s): Yes 


• Deposited: 2021-02-20 Released: 2021-11-17 
• Deposition Author(s): Sun, Y., Wang, L., Wang, N., Feng, R., Wang, X.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-based development of three- and four-antibody cocktails against SARS-CoV-2 via multiple mechanisms.

Sun, Y., Wang, L., Feng, R., Wang, N., Wang, Y., Zhu, D., Xing, X., Yang, P., Zhang, Y., Li, W., Wang, X.

(2021) Cell Res 31: 597-600

• PubMed: 33782529 
• DOI: https://doi.org/10.1038/s41422-021-00497-7
• Primary Citation Related Structures: 
  7E5R, 7E5S

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Organizational Affiliation: 
• CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310000, China. [e-mail].
Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China. [e-mail].
CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510200, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 19-mer - A3B3C3D2E2F2G2H1I1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 19-mer - A16B3 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - B3C3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 682.39 kDa 
• Atom Count: 38,916 
• Modeled Residue Count: 5,038 
• Deposited Residue Count: 6,186 
• Unique protein chains: 9

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,281	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H014 light chain	D, F [auth H]	210	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H014 heavy chain	E, J [auth L]	223	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
P17 heavy chain	G [auth I], H [auth J]	120	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
P17 light chain	I [auth K], Q [auth T]	108	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
FC05 light chain	K [auth N], N [auth Q], P [auth S]	109	Homo sapiens	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
HB27 light chain	L [auth O]	111	Homo sapiens	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
FC05 heavy chain	M [auth P], R [auth U], S [auth V]	120	Homo sapiens	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
HB27 heavy chain	O [auth R]	223	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], T [auth F], U [auth G], V [auth M], W, X, Y, Z	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Sun, Y., Wang, L., Wang, N., Feng, R., Wang, X.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB29010000

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Structure summary