7C2J

Crystal structure of nsp16-nsp10 heterodimer from SARS-CoV-2 in complex with SAM (without additional SAM during crystallization)

• PDB DOI: https://doi.org/10.2210/pdb7C2J/pdb

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


• Deposited: 2020-05-07 Released: 2020-05-27 
• Deposition Author(s): Lin, S., Chen, H., Ye, F., Chen, Z.M., Yang, F.L., Zheng, Y., Cao, Y., Qiao, J.X., Yang, S.Y., Lu, G.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 nsp10/nsp16 2'-O-methylase and its implication on antiviral drug design.

Lin, S., Chen, H., Ye, F., Chen, Z., Yang, F., Zheng, Y., Cao, Y., Qiao, J., Yang, S., Lu, G.

(2020) Signal Transduct Target Ther 5: 131-131

• PubMed: 32728018 
• DOI: https://doi.org/10.1038/s41392-020-00241-4
• Primary Citation of Related Structures:  
  7C2I, 7C2J

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Organizational Affiliation: 

West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and Collaborative Innovation Center of Biotherapy, Sichuan University, 610041, Chengdu, Sichuan, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.06 kDa 
• Atom Count: 3,323 
• Modelled Residue Count: 413 
• Deposited Residue Count: 449 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase	A	305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.1.1
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 10	B	144	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN (Subject of Investigation/LOI)	D [auth B], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.534	α = 90
b = 167.534	β = 90
c = 51.69	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Lin, S., Chen, H., Ye, F., Chen, Z.M., Yang, F.L., Zheng, Y., Cao, Y., Qiao, J.X., Yang, S.Y., Lu, G.W.

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Structure summary
• Version 1.2: 2020-09-02
  Changes: Database references
• Version 1.3: 2021-03-10
  Changes: Structure summary
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description