9EUN

SARS-CoV-2 nsp10-16 methyltransferase in complex with SAM and m7GTP

• PDB DOI: https://doi.org/10.2210/pdb9EUN/pdb

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


• Deposited: 2024-03-27 Released: 2024-05-01 
• Deposition Author(s): Kremling, V., Sprenger, J., Oberthuer, D., Scheer, T.E.S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.234 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug development

Kremling, V., Falke, S., Fernandez-Garcia, Y., Ehrt, C., Kiene, A., Klopprogge, B., Scheer, T.E.S., Barthels, F., Middendorf, P., Kuehn, S., Guenther, S., Rarey, M., Chapman, H.N., Oberthuer, D., Sprenger, J.

To be published.

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: SAXS

Macromolecule Content

• Total Structure Weight: 50.96 kDa 
• Atom Count: 3,525 
• Modelled Residue Count: 416 
• Deposited Residue Count: 444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase nsp16	A	304	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.1.1.57
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	140	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGP (Subject of Investigation/LOI)	E [auth A]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE C11 H19 N5 O14 P3 DKVRNHPCAOHRSI-KQYNXXCUSA-O
SAM	D [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
MES	C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.234 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.55	α = 90
b = 167.55	β = 90
c = 52.05	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	refinement
Coot	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Kremling, V., Sprenger, J., Oberthuer, D., Scheer, T.E.S.

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Funding Organization	Location	Grant Number
Not funded	Germany	DESY Strategy Fund MUXCOSDYN

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release