7U2D | pdb_00007u2d

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADG20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 
    0.259 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7U2D

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

A broad and potent neutralization epitope in SARS-related coronaviruses.

Yuan, M.Zhu, X.He, W.T.Zhou, P.Kaku, C.I.Capozzola, T.Zhu, C.Y.Yu, X.Liu, H.Yu, W.Hua, Y.Tien, H.Peng, L.Song, G.Cottrell, C.A.Schief, W.R.Nemazee, D.Walker, L.M.Andrabi, R.Burton, D.R.Wilson, I.A.

(2022) Proc Natl Acad Sci U S A 119: e2205784119-e2205784119

  • DOI: https://doi.org/10.1073/pnas.2205784119
  • Primary Citation Related Structures: 
    7U2D, 7U2E

  • PubMed Abstract: 

    Many neutralizing antibodies (nAbs) elicited to ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through natural infection and vaccination have reduced effectiveness to SARS-CoV-2 variants. Here, we show that therapeutic antibody ADG20 is able to neutralize SARS-CoV-2 variants of concern (VOCs) including Omicron (B.1.1.529) as well as other SARS-related coronaviruses. We delineate the structural basis of this relatively escape-resistant epitope that extends from one end of the receptor binding site (RBS) into the highly conserved CR3022 site. ADG20 can then benefit from high potency through direct competition with ACE2 in the more variable RBS and interaction with the more highly conserved CR3022 site. Importantly, antibodies that are able to target this site generally neutralize a broad range of VOCs, albeit with reduced potency against Omicron. Thus, this conserved and vulnerable site can be exploited for the design of universal vaccines and therapeutic antibodies.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.

Macromolecule Content 

  • Total Structure Weight: 71.09 kDa 
  • Atom Count: 4,873 
  • Modeled Residue Count: 628 
  • Deposited Residue Count: 650 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1205Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ADG20 heavy chainB [auth H]227Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ADG20 light chainC [auth L]218Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CIT

Query on CIT



Download:Ideal Coordinates CCD File
J [auth L]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth H],
G [auth H],
H,
I [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free:  0.259 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.083α = 90
b = 101.083β = 90
c = 80.607γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary