6WTC

Crystal Structure of the Second Form of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2

• PDB DOI: https://doi.org/10.2210/pdb6WTC/pdb

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


• Deposited: 2020-05-02 Released: 2020-05-13 
• Deposition Author(s): Wilamowski, M., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., 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: 1.85 Å
• R-Value Free: 0.214 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Crystal Structure of the Second Form of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2

Wilamowski, M., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., 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: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 46.19 kDa 
• Atom Count: 3,023 
• Modelled Residue Count: 378 
• Deposited Residue Count: 416 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	A, C	86	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B, D	122	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	E [auth B], F [auth C]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.214 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.59	α = 90
b = 120.081	β = 91.953
c = 43.309	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Wilamowski, M., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Michalska, K., Joachimiak, A., 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	--

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Structure summary
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary