7CWU | pdb_00007cwu

SARS-CoV-2 spike proteins trimer in complex with P17 and FC05 Fabs cocktail

• PDB DOI: https://doi.org/10.2210/pdb7CWU/pdb
• EM Map EMD-30488: EMDB EMDataResource

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


• Deposited: 2020-08-31 Released: 2020-12-16 
• Deposition Author(s): Wang, X., Wang, N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-based development of human antibody cocktails against SARS-CoV-2.

Wang, N., Sun, Y., Feng, R., Wang, Y., Guo, Y., Zhang, L., Deng, Y.Q., Wang, L., Cui, Z., Cao, L., Zhang, Y.J., Li, W., Zhu, F.C., Qin, C.F., Wang, X.

(2021) Cell Res 31: 101-103

• PubMed: 33262454 
• DOI: https://doi.org/10.1038/s41422-020-00446-w
• Primary Citation Related Structures: 
  7CWS, 7CWT, 7CWU

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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.
State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China.
National Health Commission of the People's Republic of China, Key laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing, Jiangsu, 210009, China.
Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310000, China.
Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China. [e-mail].
National Health Commission of the People's Republic of China, Key laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing, Jiangsu, 210009, China. [e-mail].
State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, 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].
Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510200, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 15-mer - A3B3C3D3E3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 15-mer - A12B3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 581.73 kDa 
• Atom Count: 36,128 
• Modeled Residue Count: 4,592 
• Deposited Residue Count: 5,190 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of FC05 Fab	A [auth P], C [auth N], E [auth J]	120	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of FC05 Fab	B [auth I], D [auth G], F	109	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	G [auth B], H [auth C], I [auth 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
Glycosylation
Glycosylation Sites: 10		Go to GlyGen: P0DTC2-1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of P17 Fab	J [auth H], L [auth M], N [auth O]	120	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of P17 Fab	K [auth L], M [auth R], O [auth S]	108	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 6
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], P [auth D], Q [auth E], R [auth K], S [auth Q], T, U, V, W, X, Y, Z	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Wang, X., Wang, N.

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2021-01-13
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary