7F12

A SARS-CoV-2 neutralizing antibody

• PDB DOI: https://doi.org/10.2210/pdb7F12/pdb

• Classification: VIRAL PROTEIN/ANTIVIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-06-07 Released: 2022-06-15 
• Deposition Author(s): Zhang, G., Li, X., Guo, Y., Wang, Y., Yuan, S.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.245 
• R-Value Work: 0.195 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

A SARS-CoV-2 neutralizing antibody

Zhang, G., Li, X., Guo, Y., Wang, Y., Yuan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.88 kDa 
• Atom Count: 3,159 
• Modelled Residue Count: 399 
• Deposited Residue Count: 459 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	206	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
Antibody	B	253	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.245 
• R-Value Work: 0.195 
• R-Value Observed: 0.200 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.46	α = 90
b = 75.46	β = 90
c = 184.135	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Zhang, G., Li, X., Guo, Y., Wang, Y., Yuan, S.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2018YFE0200402

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary