7E3K | pdb_00007e3k

Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7E3K

This is version 1.2 of the entry. See complete history

Literature

Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants.

Li, T.Han, X.Gu, C.Guo, H.Zhang, H.Wang, Y.Hu, C.Wang, K.Liu, F.Luo, F.Zhang, Y.Hu, J.Wang, W.Li, S.Hao, Y.Shen, M.Huang, J.Long, Y.Song, S.Wu, R.Mu, S.Chen, Q.Gao, F.Wang, J.Long, S.Li, L.Wu, Y.Gao, Y.Xu, W.Cai, X.Qu, D.Zhang, Z.Zhang, H.Li, N.Gao, Q.Zhang, G.He, C.Wang, W.Ji, X.Tang, N.Yuan, Z.Xie, Y.Yang, H.Zhang, B.Huang, A.Jin, A.

(2021) Nat Commun 12: 6304-6304

  • DOI: https://doi.org/10.1038/s41467-021-26539-7
  • Primary Citation Related Structures: 
    7E3K, 7E3L

  • PubMed Abstract: 

    Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor binding domain (RBD) specific monoclonal antibodies (mAbs), 58G6, 510A5 and 13G9, with high neutralizing potency blocking authentic SARS-CoV-2 virus display remarkable efficacy against authentic B.1.351 virus. Surprisingly, structural analysis has revealed that 58G6 and 13G9 both recognize the steric region S 470-495 on the RBD, overlapping the E484K mutation presented in B.1.351. Also, 58G6 directly binds to another region S 450-458 in the RBD. Significantly, 58G6 and 510A5 both demonstrate prophylactic efficacy against authentic SARS-CoV-2 and B.1.351 viruses in the transgenic mice expressing human ACE2 (hACE2), protecting weight loss and reducing virus loads. Together, we have evidenced 2 potent neutralizing Abs with unique mechanism targeting authentic SARS-CoV-2 mutants, which can be promising candidates to fulfill the urgent needs for the prolonged COVID-19 pandemic.


  • Organizational Affiliation
    • Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, 400010, China.

Macromolecule Content 

  • Total Structure Weight: 573.28 kDa 
  • Atom Count: 32,539 
  • Modeled Residue Count: 4,278 
  • Deposited Residue Count: 5,172 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 8Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
13G9 heavy chain
D, F, H
221Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
13G9 light chainE,
G,
I [auth L]
215Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth C],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary