7BWQ | pdb_00007bwq

Structure of nonstructural protein Nsp9 from SARS-CoV-2

PDB DOI: https://doi.org/10.2210/pdb7BWQ/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2020-04-15 Released: 2021-07-21
Deposition Author(s): Zhang, C., Chen, Y., Li, L., Su, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.299 (Depositor), 0.299 (DCC)
R-Value Work:
0.213 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2.

Zhang, C., Chen, Y., Li, L., Yang, Y., He, J., Chen, C., Su, D.

(2020) Mol Biomed 1: 5-5

DOI: https://doi.org/10.1186/s43556-020-00005-0

Macromolecule Content

Total Structure Weight: 74.83 kDa
Atom Count: 5,054
Modeled Residue Count: 645
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nsp9	A B C D E [auth F] A, B, C, D, E [auth F], F [auth E]	113	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain K [auth F] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth F] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth F] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	G [auth A], H [auth A], I [auth B], J [auth C], K [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.299 (Depositor), 0.299 (DCC)
R-Value Work: 0.213 (Depositor), 0.220 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.713	α = 90
b = 134.445	β = 90
c = 166.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-07-21
Type: Initial release
Version 1.1: 2022-02-16
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, 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.