7L6R

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and Manganese (Mn).

• PDB DOI: https://doi.org/10.2210/pdb7L6R/pdb
• NAKB: 7L6R

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


• Deposited: 2020-12-23 Released: 2021-01-06 
• Deposition Author(s): Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.166 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 52.47 kDa 
• Atom Count: 3,873 
• Modelled Residue Count: 415 
• Deposited Residue Count: 448 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase	A	300	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	141	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

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*UP*AP*A)-3')	C	7	synthetic construct

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	H [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
BDF	N [auth B]	beta-D-fructopyranose C6 H12 O6 LKDRXBCSQODPBY-ARQDHWQXSA-N
GLC	I [auth A], J [auth A], K [auth A], L [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.166 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.757	α = 90
b = 168.757	β = 90
c = 52.272	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-06 
Deposition Author(s): Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2021-01-06
  Type: Initial release
  
• Version 1.1: 2021-01-20
  Changes: Experimental preparation
• Version 1.2: 2021-12-15
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.0: 2024-03-06
  Changes: Data collection, Non-polymer description, Structure summary