7CWM

Complex of SARS-CoV-2 spike protein and Fab P17 with one RBD in open state and two RBD in closed state


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Rational development of a human antibody cocktail that deploys multiple functions to confer Pan-SARS-CoVs protection.

Yao, H.Sun, Y.Deng, Y.Q.Wang, N.Tan, Y.Zhang, N.N.Li, X.F.Kong, C.Xu, Y.P.Chen, Q.Cao, T.S.Zhao, H.Yan, X.Cao, L.Lv, Z.Zhu, D.Feng, R.Wu, N.Zhang, W.Hu, Y.Chen, K.Zhang, R.R.Lv, Q.Sun, S.Zhou, Y.Yan, R.Yang, G.Sun, X.Liu, C.Lu, X.Cheng, L.Qiu, H.Huang, X.Y.Weng, T.Shi, D.Jiang, W.Shao, J.Wang, L.Zhang, J.Jiang, T.Lang, G.Qin, C.F.Li, L.Wang, X.

(2021) Cell Res 31: 25-36

  • DOI: https://doi.org/10.1038/s41422-020-00444-y
  • Primary Citation of Related Structures:  
    7CWL, 7CWM, 7CWN, 7CWO

  • PubMed Abstract: 

    Structural principles underlying the composition and synergistic mechanisms of protective monoclonal antibody cocktails are poorly defined. Here, we exploited antibody cooperativity to develop a therapeutic antibody cocktail against SARS-CoV-2. On the basis of our previously identified humanized cross-neutralizing antibody H014, we systematically analyzed a fully human naive antibody library and rationally identified a potent neutralizing antibody partner, P17, which confers effective protection in animal model. Cryo-EM studies dissected the nature of the P17 epitope, which is SARS-CoV-2 specific and distinctly different from that of H014. High-resolution structure of the SARS-CoV-2 spike in complex with H014 and P17, together with functional investigations revealed that in a two-antibody cocktail, synergistic neutralization was achieved by S1 shielding and conformational locking, thereby blocking receptor attachment and viral membrane fusion, conferring high potency as well as robustness against viral mutation escape. Furthermore, cluster analysis identified a hypothetical 3rd antibody partner for further reinforcing the cocktail as pan-SARS-CoVs therapeutics.


  • Organizational Affiliation

    State Key Laboratory for Diagnosis and Treatment of Infectious Diseases/National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,273Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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: 10Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
P17 heavy chainD [auth G],
E [auth H],
F [auth I]
120Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
P17 light chainG [auth L],
H [auth J],
I [auth K]
108Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J [auth D],
K [auth E],
L [auth F],
M,
N,
J [auth D],
K [auth E],
L [auth F],
M,
N,
O,
P,
Q,
R,
S,
T,
U,
V,
W
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth A],
BA [auth A],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
X [auth A],
Y [auth A],
Z [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: 3.60 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: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references