7JIB | pdb_00007jib

Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1

• PDB DOI: https://doi.org/10.2210/pdb7JIB/pdb

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


• Deposited: 2020-07-23 Released: 2020-08-26 
• Deposition Author(s): Wilamowski, M., Minasov, G., Kim, Y., Sherrell, D.A., Shuvalova, L., Lavens, A., Chard, R., Rosas-Lemus, M., Maltseva, N., Jedrzejczak, R., Michalska, K., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.181 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography.

Wilamowski, M., Sherrell, D.A., Minasov, G., Kim, Y., Shuvalova, L., Lavens, A., Chard, R., Maltseva, N., Jedrzejczak, R., Rosas-Lemus, M., Saint, N., Foster, I.T., Michalska, K., Satchell, K.J.F., Joachimiak, A.

(2021) Proc Natl Acad Sci U S A 118

• PubMed: 33972410 
• DOI: https://doi.org/10.1073/pnas.2100170118
• Primary Citation Related Structures: 
  6XKM, 7JHE, 7JIB, 7JPE


• PubMed Abstract: 
  

  The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5'-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2'-O position of the first nucleotide. To investigate the conformational changes of the complex during 2'-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog ( ^m7 GpppA _m2'-O ). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637.
Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology of Jagiellonian University, Krakow 30387, Poland.
Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439.
Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611.
Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439.
Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637; [e-mail].

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: 51.81 kDa 
• Atom Count: 3,583 
• Modeled Residue Count: 413 
• 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V9G (Subject of Investigation/LOI)	H [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)	G [auth A]	P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C21 H30 N10 O17 P3 QQOHNVHGNZYSBP-XPWFQUROSA-O
MGP (Subject of Investigation/LOI)	I [auth A]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE C11 H19 N5 O14 P3 DKVRNHPCAOHRSI-KQYNXXCUSA-O
SAM (Subject of Investigation/LOI)	E [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SAH (Subject of Investigation/LOI)	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN (Subject of Investigation/LOI)	J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.181 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.83	α = 90
b = 170.83	β = 90
c = 52.738	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Wilamowski, M., Minasov, G., Kim, Y., Sherrell, D.A., Shuvalova, L., Lavens, A., Chard, R., Rosas-Lemus, M., Maltseva, N., Jedrzejczak, R., Michalska, K., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description