8UD2 | pdb_00008ud2

SARS-CoV-2 Nsp15, apo-form

• PDB DOI: https://doi.org/10.2210/pdb8UD2/pdb
• EM Map EMD-42144: EMDB EMDataResource

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-09-28 Released: 2024-04-24 
• Deposition Author(s): Ito, F., Yang, H., Zhou, Z.H., Chen, X.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for polyuridine tract recognition by SARS-CoV-2 Nsp15.

Ito, F., Yang, H., Zhou, Z.H., Chen, X.S.

(2024) Protein Cell 15: 547-552

• PubMed: 38613382 
• DOI: https://doi.org/10.1093/procel/pwae009
• Primary Citation Related Structures: 
  8UD2, 8UD3, 8UD4, 8UD5

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Organizational Affiliation: 
• Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA.
California NanoSystems Institute, University of California, Los Angeles, CA90095, USA.
Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA90089, USA.
Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90089, USA.
Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA90089, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 241.25 kDa 
• Atom Count: 16,530 
• Modeled Residue Count: 2,076 
• Deposited Residue Count: 2,154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 15	A, B, C, D, E, F	359	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 4.6.1
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Ito, F., Yang, H., Zhou, Z.H., Chen, X.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI150524

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release
  
• Version 1.1: 2024-07-10
  Changes: Data collection, Database references