7KOA | pdb_00007koa

Room Temperature Structure of SARS-CoV-2 Nsp10/16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography

• PDB DOI: https://doi.org/10.2210/pdb7KOA/pdb

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


• Deposited: 2020-11-07 Released: 2020-11-18 
• Deposition Author(s): Wilamowski, M., Sherrell, D.A., Minasov, G., Shuvalova, L., Lavens, A., Henning, R., Maltseva, N., Rosas-Lemus, M., Kim, Y., Satchell, K.J.F., Srajer, V., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.277 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography

Wilamowski, M., Sherrell, D.A., Minasov, G., Shuvalova, L., Lavens, A., Henning, R., Maltseva, N., Rosas-Lemus, M., Kim, Y., Satchell, K.J.F., Srajer, V., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content 

• Total Structure Weight: 50.81 kDa 
• Atom Count: 3,571 
• Modeled Residue Count: 419 
• Deposited Residue Count: 443 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase	A	301	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	142	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTA (Subject of Investigation/LOI)	C [auth A], E [auth A]	P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C21 H30 N10 O17 P3 QQOHNVHGNZYSBP-XPWFQUROSA-O
SAM (Subject of Investigation/LOI)	D [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN (Subject of Investigation/LOI)	F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.277 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.86	α = 90
b = 170.86	β = 90
c = 52.797	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
Precognition	data reduction
Epinorm	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Wilamowski, M., Sherrell, D.A., Minasov, G., Shuvalova, L., Lavens, A., Henning, R., Maltseva, N., Rosas-Lemus, M., Kim, Y., Satchell, K.J.F., Srajer, V., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description