9MRU | pdb_00009mru

Structural Asymmetry in SARS-CoV-2 Nsp15 Hexamer Important for Catalytic Activity

PDB DOI: https://doi.org/10.2210/pdb9MRU/pdb

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

Deposited: 2025-01-08 Released: 2025-06-04
Deposition Author(s): Ketawala, G.K., Sonowal, M., Schrag, L., Fromme, R., Botha, S., Fromme, P.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.211 (Depositor), 0.202 (DCC)
R-Value Work:
0.185 (Depositor), 0.180 (DCC)
R-Value Observed:
0.198 (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

Structural Asymmetry in SARS-CoV-2 Nsp15 Hexamer Important for Catalytic Activity

Ketawala, G.K., Sonowal, M., Schrag, L., Fromme, R., Botha, S., Fromme, P.

To be published.

Macromolecule Content

Total Structure Weight: 233.96 kDa
Atom Count: 16,476
Modeled Residue Count: 2,082
Deposited Residue Count: 2,082
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate-specific endoribonuclease nsp15	A, B, C, D, E A, B, C, D, E, F	347	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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.211 (Depositor), 0.202 (DCC)
R-Value Work: 0.185 (Depositor), 0.180 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.7	α = 90
b = 116.6	β = 119.4
c = 154.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
PDB-REDO	refinement
CrystFEL	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	STC-1231306
National Science Foundation (NSF, United States)	United States	2031343

Revision History (Full details and data files)

Version 1.0: 2025-06-04
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.