9C7X | pdb_00009c7x

Crystal structure of SARS-CoV-2 antibody 1H06 in complex with a HR2 peptide

• PDB DOI: https://doi.org/10.2210/pdb9C7X/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens, synthetic construct
• Mutation(s): Yes 


• Deposited: 2024-06-11 Released: 2025-06-18 
• Deposition Author(s): Van Wazer, D.J., Zhou, T., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: in silico

Literature

SARS-CoV-2 Peptide Immunization in Mice Elicits Broadly Neutralizing Antibodies Targeting Cryptic S2 Helical-Stem Epitope

Sastry, M.

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: 49.46 kDa 
• Atom Count: 3,819 
• Modeled Residue Count: 455 
• Deposited Residue Count: 455 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain of SARS-CoV-2 antibody 1H06	A	216	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of SARS-CoV-2 antibody 1H06	B	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	C	20	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.983	α = 90
b = 142.498	β = 90
c = 54.262	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Van Wazer, D.J., Zhou, T., Kwong, P.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release