7F0X

A SARS-CoV-2 neutralizing antibody

PDB DOI: https://doi.org/10.2210/pdb7F0X/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.270
R-Value Work: 0.221
R-Value Observed: 0.226

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A SARS-CoV-2 neutralizing antibody

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

To be published.

Macromolecule Content

Total Structure Weight: 49.23 kDa
Atom Count: 3,238
Modelled Residue Count: 411
Deposited Residue Count: 447
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	194	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence AnnotationsExpand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody	B	253	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence AnnotationsExpand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.270
R-Value Work: 0.221
R-Value Observed: 0.226
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.369	α = 90
b = 75.369	β = 90
c = 186.632	γ = 120

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-06-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-06-15
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.