8XZ4 | pdb_00008xz4

SARS-CoV-2 S and radixin complex structure

PDB DOI: https://doi.org/10.2210/pdb8XZ4/pdb

Classification: VIRAL PROTEIN/PROEIN BINDING
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-20 Released: 2025-10-08
Deposition Author(s): Wang, J.M., Ma, W.F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.266 (Depositor), 0.268 (DCC)
R-Value Work:
0.216 (Depositor), 0.223 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

SARS-CoV-2 S and radixin complex structure

Wang, J.M., Ma, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 36.77 kDa
Atom Count: 2,634
Modeled Residue Count: 306
Deposited Residue Count: 310
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Radixin	A	296	Homo sapiens	Mutation(s): 0 Gene Names: RDX
UniProt & NIH Common Fund Data Resources
Find proteins for P35241 (Homo sapiens) Explore P35241 Go to UniProtKB: P35241
PHAROS: P35241 GTEx: ENSG00000137710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35241
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	B	14	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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 Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.266 (Depositor), 0.268 (DCC)
R-Value Work: 0.216 (Depositor), 0.223 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.375	α = 90
b = 77.375	β = 90
c = 58.444	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.