8CWI

Fab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD)

• PDB DOI: https://doi.org/10.2210/pdb8CWI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-05-19 Released: 2023-05-24 
• Deposition Author(s): Langley, D.B., Christ, D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.205 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Neutralization of CoV-2 omicron lineages by affinity-matured class 5 antibodies

Langley, D.B., Christ, D.

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.82 kDa 
• Atom Count: 5,666 
• Modelled Residue Count: 627 
• Deposited Residue Count: 647 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	204	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab arm of antibody 10G4	B [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab arm of antibody 10G4	C [auth L]	215	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	G [auth H], H, J [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A], I [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.205 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.691	α = 90
b = 88.639	β = 95.03
c = 81.398	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Langley, D.B., Christ, D.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary