7Z0Y | pdb_00007z0y

THSC20.HVTR04 Fab bound to SARS-CoV-2 Receptor Binding Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.241 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

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

Validation slider image for 7Z0Y

This is version 1.3 of the entry. See complete history

Literature

A combination of potently neutralizing monoclonal antibodies isolated from an Indian convalescent donor protects against the SARS-CoV-2 Delta variant.

Hingankar, N.Deshpande, S.Das, P.Rizvi, Z.A.Wibmer, C.K.Mashilo, P.Ansari, M.Y.Burns, A.Barman, S.Zhao, F.Mukherjee, S.Torres, J.L.Chattopadhyay, S.Mehdi, F.Sutar, J.Rathore, D.K.Pargai, K.Singh, J.Sonar, S.Jakhar, K.Dandotiya, J.Bhattacharyya, S.Mani, S.Samal, S.Singh, S.Kshetrapal, P.Thiruvengadam, R.Batra, G.Medigeshi, G.Ward, A.B.Bhatnagar, S.Awasthi, A.Sok, D.Bhattacharya, J.

(2022) PLoS Pathog 18: e1010465-e1010465

  • DOI: https://doi.org/10.1371/journal.ppat.1010465
  • Primary Citation Related Structures: 
    7Z0X, 7Z0Y

  • PubMed Abstract: 

    Although efficacious vaccines have significantly reduced the morbidity and mortality of COVID-19, there remains an unmet medical need for treatment options, which monoclonal antibodies (mAbs) can potentially fill. This unmet need is exacerbated by the emergence and spread of SARS-CoV-2 variants of concern (VOCs) that have shown some resistance to vaccine responses. Here we report the isolation of five neutralizing mAbs from an Indian convalescent donor, out of which two (THSC20.HVTR04 and THSC20.HVTR26) showed potent neutralization of SARS-CoV-2 VOCs at picomolar concentrations, including the Delta variant (B.1.617.2). One of these (THSC20.HVTR26) also retained activity against the Omicron variant. These two mAbs target non-overlapping epitopes on the receptor-binding domain (RBD) of the spike protein and prevent virus attachment to its host receptor, human angiotensin converting enzyme-2 (hACE2). Furthermore, the mAb cocktail demonstrated protection against the Delta variant at low antibody doses when passively administered in the K18 hACE2 transgenic mice model, highlighting their potential as a cocktail for prophylactic and therapeutic applications. Developing the capacity to rapidly discover and develop mAbs effective against highly transmissible pathogens like coronaviruses at a local level, especially in a low- and middle-income country (LMIC) such as India, will enable prompt responses to future pandemics as an important component of global pandemic preparedness.


  • Organizational Affiliation
    • IAVI HIV Vaccine Translational Research Laboratory, IAVI-THSTI partnership program, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, India.

Macromolecule Content 

  • Total Structure Weight: 71.23 kDa 
  • Atom Count: 4,931 
  • Modeled Residue Count: 633 
  • Deposited Residue Count: 652 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
THSC20.HVTR04 Fab heavy chainA [auth H]233Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
THSC20.HVTR04 Fab light chainB [auth L]214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1C [auth R]205Severe 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: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth H]L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.241 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.157α = 90
b = 126.157β = 90
c = 167.454γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2022-04-13 
  • Deposition Author(s): Wibmer, C.K.

Funding OrganizationLocationGrant Number
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)United States3R21TW011454-02S1

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary