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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36w4b

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

Entry History & Funding Information

Deposition Data

• Released Date: 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)

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

Revision History  

• 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