9EMV | pdb_00009emv

SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin and m7GpppA (Cap0-analog)/m7GpppAm (Cap1-analog)

• PDB DOI: https://doi.org/10.2210/pdb9EMV/pdb

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


• Deposited: 2024-03-11 Released: 2024-03-20 
• 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: 2.34 Å
• R-Value Free: 
  0.256 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

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

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

(2024) Elife 

• DOI: https://doi.org/10.7554/elife.98310.1

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: 52.12 kDa 
• Atom Count: 3,585 
• Modeled Residue Count: 415 
• 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V9G (Subject of Investigation/LOI)	M [auth A]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE C22 H32 N10 O17 P3 WZAAWBDISKLAIE-NAGRZYTCSA-N
GTA (Subject of Investigation/LOI)	D [auth A]	P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C21 H30 N10 O17 P3 QQOHNVHGNZYSBP-XPWFQUROSA-O
SAH	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SGV (Subject of Investigation/LOI)	C [auth A]	SANGIVAMYCIN C12 H15 N5 O5 OBZJZDHRXBKKTJ-JTFADIMSSA-N
MES	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.256 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.51	α = 90
b = 169.51	β = 90
c = 52.25	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: 2024-03-20 
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: 2024-03-20
  Type: Initial release
  
• Version 2.0: 2024-11-13
  Changes: Atomic model, Data collection, Database references, Structure summary