8F2X

Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain

• PDB DOI: https://doi.org/10.2210/pdb8F2X/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-11-08 Released: 2024-04-17 
• Deposition Author(s): Sankhala, R.S., Joyce, G.M.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.324 
• R-Value Work: 0.245 
• R-Value Observed: 0.248 

Literature

Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain

Sankhala, R.S., Jensen, J., Modjarrad, K., Nelson, M., Joyce, M.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 71.6 kDa 
• Atom Count: 4,862 
• Modelled Residue Count: 629 
• Deposited Residue Count: 651 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WRAIR-2123 Fab Heavy chain	B [auth H]	232	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
WRAIR-2123 Fab Light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.324 
• R-Value Work: 0.245 
• R-Value Observed: 0.248 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.29	α = 90
b = 94.43	β = 90
c = 201.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Sankhala, R.S., Joyce, G.M.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	W81XWH-07-2-0067

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release