6W4B | pdb_00006w4b

The crystal structure of Nsp9 RNA binding protein of SARS CoV-2

PDB DOI: https://doi.org/10.2210/pdb6W4B/pdb

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

Deposited: 2020-03-10 Released: 2020-03-18
Deposition Author(s): Tan, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Michalska, K., Joachimiak, A., 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: 2.95 Å
R-Value Free:
0.276 (Depositor), 0.283 (DCC)
R-Value Work:
0.240 (Depositor), 0.247 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of Nsp9 replicase protein of COVID-19

Tan, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 25.59 kDa
Atom Count: 1,685
Modeled Residue Count: 225
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 9	A, B	117	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.276 (Depositor), 0.283 (DCC)
R-Value Work: 0.240 (Depositor), 0.247 (DCC)
R-Value Observed: 0.242 (Depositor)

Diffraction Data:

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.883	α = 90
b = 89.883	β = 90
c = 132.587	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	refinement
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Jedrzejczak, R.

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: 2020-03-18
Type: Initial release
Version 1.1: 2020-03-25
Changes: Source and taxonomy, Structure summary
Version 1.2: 2020-05-06
Changes: Database references, Source and taxonomy, Structure summary
Version 1.3: 2023-10-18
Changes: Data collection, Database references, 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.