7T9W | pdb_00007t9w

Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2

PDB DOI: https://doi.org/10.2210/pdb7T9W/pdb

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

Deposited: 2021-12-20 Released: 2021-12-29
Deposition Author(s): Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.316 (Depositor), 0.314 (DCC)
R-Value Work:
0.262 (Depositor), 0.261 (DCC)
R-Value Observed:
0.263 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2

Stogios, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 182.41 kDa
Atom Count: 11,883
Modeled Residue Count: 1,430
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	105	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain S [auth H] MOL2 format, chain R [auth D] MOL2 format, chain S [auth H] mmCIF format, chain R [auth D] mmCIF format, chain S [auth H]	R [auth D], S [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth D] Focus chain S [auth H] Interactions & Density Focus chain R [auth D] Focus chain S [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.316 (Depositor), 0.314 (DCC)
R-Value Work: 0.262 (Depositor), 0.261 (DCC)
R-Value Observed: 0.263 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.462	α = 90
b = 157.462	β = 90
c = 79.619	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-29

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2021-12-29
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection
Version 1.2: 2024-04-03
Changes: Refinement description

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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.