Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 99.97 kDa 
• Atom Count: 4985 
• Modelled Residue Count: 635 
• Deposited Residue Count: 900 
• Unique protein chains: 3

7CM4

Crystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59

• PDB DOI: 10.2210/pdb7CM4/pdb

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


• Deposited: 2020-07-24 Released: 2021-01-20 
• Deposition Author(s): Kim, Y.G., Jeong, J.H., Bae, J.S., Lee, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.242 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein.

Kim, C., Ryu, D.K., Lee, J., Kim, Y.I., Seo, J.M., Kim, Y.G., Jeong, J.H., Kim, M., Kim, J.I., Kim, P., Bae, J.S., Shim, E.Y., Lee, M.S., Kim, M.S., Noh, H., Park, G.S., Park, J.S., Son, D., An, Y., Lee, J.N., Kwon, K.S., Lee, J.Y., Lee, H., Yang, J.S., Kim, K.C., Kim, S.S., Woo, H.M., Kim, J.W., Park, M.S., Yu, K.M., Kim, S.M., Kim, E.H., Park, S.J., Jeong, S.T., Yu, C.H., Song, Y., Gu, S.H., Oh, H., Koo, B.S., Hong, J.J., Ryu, C.M., Park, W.B., Oh, M.D., Choi, Y.K., Lee, S.Y.

(2021) Nat Commun 12: 288-288

• PubMed: 33436577 
• DOI: 10.1038/s41467-020-20602-5
• Primary Citation of Related Structures:  
  7CM4


• PubMed Abstract: 
  

Vaccines and therapeutics are urgently needed for the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we screen human monoclonal antibodies (mAb) targeting the receptor binding domain (RBD) of the viral spike protein via antibody library constructed from peripheral blood mononuclear cells of a convalescent patient. The CT-P59 mAb potently neutralizes SARS-CoV-2 isolates including the D614G variant without antibody-dependent enhancement effect. Complex crystal structure of CT-P59 Fab/RBD shows that CT-P59 blocks interaction regions of RBD for angiotensin converting enzyme 2 (ACE2) receptor with an orientation that is notably different from previously reported RBD-targeting mAbs. Furthermore, therapeutic effects of CT-P59 are evaluated in three animal models (ferret, hamster, and rhesus monkey), demonstrating a substantial reduction in viral titer along with alleviation of clinical symptoms. Therefore, CT-P59 may be a promising therapeutic candidate for COVID-19.

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Organizational Affiliation: 

Biotechnology Research Institute, Celltrion Inc, Incheon, 22014, Republic of Korea. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	226	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
IgG heavy chain	B [auth H]	458	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG light chain	C [auth L]	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G17392HI GlyCosmos:  G17392HI GlyGen:  G17392HI

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth L], G [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	E [auth H], H [auth L]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.242 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.55	α = 90
b = 167.6	β = 90
c = 169.05	γ = 90

Software Package:

Software Name	Purpose
Coot	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-07-24 
• Released Date: 2021-01-20 
Deposition Author(s): Kim, Y.G., Jeong, J.H., Bae, J.S., Lee, J.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references, Structure summary