7NAB

Crystal structure of human neutralizing mAb CV3-25 binding to SARS-CoV-2 S MPER peptide 1140-1165


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern.

Li, W.Chen, Y.Prevost, J.Ullah, I.Lu, M.Gong, S.Y.Tauzin, A.Gasser, R.Vezina, D.Anand, S.P.Goyette, G.Chaterjee, D.Ding, S.Tolbert, W.D.Grunst, M.W.Bo, Y.Zhang, S.Richard, J.Zhou, F.Huang, R.K.Esser, L.Zeher, A.Cote, M.Kumar, P.Sodroski, J.Xia, D.Uchil, P.D.Pazgier, M.Finzi, A.Mothes, W.

(2022) Cell Rep 38: 110210-110210

  • DOI: https://doi.org/10.1016/j.celrep.2021.110210
  • Primary Citation of Related Structures:  
    7NAB

  • PubMed Abstract: 

    Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating continued refinement of antibody therapies and immunogen design. Here, we elucidate the structural basis and mode of action for two potent SARS-CoV-2 spike (S)-neutralizing monoclonal antibodies, CV3-1 and CV3-25, which remain effective against emerging variants of concern in vitro and in vivo. CV3-1 binds to the (485-GFN-487) loop within the receptor-binding domain (RBD) in the "RBD-up" position and triggers potent shedding of the S1 subunit. In contrast, CV3-25 inhibits membrane fusion by binding to an epitope in the stem helix region of the S2 subunit that is highly conserved among β-coronaviruses. Thus, vaccine immunogen designs that incorporate the conserved regions in the RBD and stem helix region are candidates to elicit pan-coronavirus protective immune responses.


  • Organizational Affiliation

    Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CV3-25 Fab Heavy ChainA [auth H],
C [auth A]
227Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CV3-25 Fab Light ChainB [auth L],
D [auth B]
213Homo 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
Spike protein S2E [auth D],
F [auth C]
27Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
W [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth H]
H
I [auth H]
J [auth L]
K [auth L]
G [auth H],
H,
I [auth H],
J [auth L],
K [auth L],
L,
M [auth L],
N [auth L],
O [auth L],
P [auth L],
Q [auth A],
R [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.762α = 90
b = 85.241β = 114.77
c = 87.067γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesStart-up funds from the Uniformed Services University of the Health Sciences

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references
  • Version 1.2: 2022-01-19
    Changes: Database references
  • Version 1.3: 2022-01-26
    Changes: Database references
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary