9NQ3 | pdb_00009nq3

Crystal structure of SARS-CoV-2 S2 directed Fab 1871

• PDB DOI: https://doi.org/10.2210/pdb9NQ3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-03-11 Released: 2025-11-12 
• Deposition Author(s): Muthuraman, K., Ivanochko, D., Julien, J.P.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: in silico

Literature

cryo-EM structure of broad betacoronavirus binding antibody 1871 in complex with OC43 S2 subunit

Muthuraman, K., Jackman, M.J., Julien, J.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 95.47 kDa 
• Atom Count: 6,644 
• Modeled Residue Count: 882 
• Deposited Residue Count: 884 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1871 Fab heavy chain	A [auth H], C [auth A]	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1871 Fab light chain	B [auth L], D [auth B]	215	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.192	α = 90
b = 101.333	β = 90
c = 134.982	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XPREP	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Muthuraman, K., Ivanochko, D., Julien, J.P.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-023398

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release