8XAB

Crystal structure of Ubl1 domain of nonstructural protein 3 of SARS-CoV-2

PDB DOI: https://doi.org/10.2210/pdb8XAB/pdb

Classification: VIRUS
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-03 Released: 2023-12-20
Deposition Author(s): Li, Y., Ke, Z.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.234
R-Value Work: 0.210
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

N-terminus of SARS-CoV-2 Nsp3 Interrupts RNA-driven Phase Separation of N Protein by Displacing RNA

Ke, Z., Zhang, H., Wang, Y., Wang, J.N., Peng, F., Wang, J., Liu, X., Hu, H., Li, Y.

To be published.

Macromolecule Content

Total Structure Weight: 11.15 kDa
Atom Count: 878
Modelled Residue Count: 95
Deposited Residue Count: 96
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	96	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.234
R-Value Work: 0.210
R-Value Observed: 0.211
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.911	α = 90
b = 98.377	β = 90
c = 27.883	γ = 90

Software Package:

Software Name	Purpose
DIALS	data reduction
DIALS	data scaling
PHASER	phasing
PHENIX	refinement
PHENIX	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.