8UD5

SARS-CoV-2 Nsp15 bound to poly(A/U) RNA, state 2

PDB DOI: https://doi.org/10.2210/pdb8UD5/pdb
EM Map EMD-42147: EMDB EMDataResource
NAKB: 8UD5

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

Organizational Affiliation

Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

Macromolecule Content

Total Structure Weight: 263.49 kDa
Atom Count: 17,664
Modelled Residue Count: 2,130
Deposited Residue Count: 2,224
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 15	A [auth F] B [auth D] C [auth E] D [auth B] E [auth A] A [auth F], B [auth D], C [auth E], D [auth B], E [auth A], F [auth C]	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (35-MER)	G	35	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (35-MER)	H	35	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

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

Revision History (Full details and data files)

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

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.