8CWJ

Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain (pRBD)

• PDB DOI: https://doi.org/10.2210/pdb8CWJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Pangolin coronavirus
• 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.230 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

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 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 242.85 kDa 
• Atom Count: 16,808 
• Modelled Residue Count: 2,121 
• Deposited Residue Count: 2,198 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of CR3022 antibody Fab	A [auth H], D [auth A]	230	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of CR3022 antibody Fab	B [auth L], E [auth B]	220	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth G], F [auth I]	204	Pangolin coronavirus	Mutation(s): 0
UniProt
Find proteins for A0A7D6PMV8 (Pangolin coronavirus) Explore A0A7D6PMV8  Go to UniProtKB:  A0A7D6PMV8
Glycosylation
Glycosylation Sites: 2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of 4C12-B12 antibody Fab	G [auth J], I [auth U]	230	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of 4C12-B12 antibody Fab	H [auth K], J [auth V]	215	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
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	K [auth C], L [auth D], M [auth E]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	DA [auth J], EA [auth J], GA [auth K], IA [auth U], KA [auth V], LA [auth V], MA [auth V], N [auth H], O [auth G], Q [auth G], U [auth I], V [auth I], W [auth I], X [auth I], Y [auth I]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	AA [auth I], BA [auth I], CA [auth I], FA [auth J], HA [auth K], JA [auth U], R [auth G], S [auth G], T [auth G], Z [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.230 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.433	α = 90
b = 144.097	β = 117.51
c = 168.842	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.

---

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