8QH0

Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194

• PDB DOI: https://doi.org/10.2210/pdb8QH0/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Drosophila melanogaster, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-09-06 Released: 2024-06-19 
• Deposition Author(s): Fernandez, I., Rey, F.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.209 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Starting Models: experimental, in silico

Literature

A broadly neutralizing antibody against SARS-CoV-2 Omicron variants

Planchais, C., Fernandez, I., Rey, F.A., Mouquet, H.

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: 70.99 kDa 
• Atom Count: 5,154 
• Modelled Residue Count: 618 
• Deposited Residue Count: 646 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	206	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cv2.3194 Heavy chain	B [auth H]	229	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IGK@ protein	C [auth L]	211	Homo sapiens	Mutation(s): 0  Gene Names: IGK@
UniProt
Find proteins for Q6PJF2 (Homo sapiens) Explore Q6PJF2  Go to UniProtKB:  Q6PJF2

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRO	E [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
GOL	F [auth A], G [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.209 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.388	α = 90
b = 89.186	β = 90
c = 174.471	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Fernandez, I., Rey, F.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary