7DOK

Structure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir

• PDB DOI: https://doi.org/10.2210/pdb7DOK/pdb
• NAKB: 7DOK
• EM Map EMD-30795: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-12-14 Released: 2021-12-15 
• Deposition Author(s): Li, Z., Yu, X.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for repurpose and design of nucleotide drugs for treating COVID-19

Yin, W., Luan, X., Li, Z., Xie, Y., Zhou, Z., Liu, J., Gao, M., Wang, X., Zhou, F., Wang, Q., Wang, Q., Shen, D., Zhang, Y., Tian, G., Aisa, H., Wei, D., Jiang, Y., Xiao, G., Jiang, H., Zhang, L., Yu, X., Shen, J., Zhang, S., Xu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 176.26 kDa 
• Atom Count: 11,534 
• Modelled Residue Count: 1,367 
• Deposited Residue Count: 1,469 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	C [auth A]	943	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.7.7.48
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	D [auth B], F [auth G]	199	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	E [auth C]	84	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: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3')	A [auth P]	20	Severe acute respiratory syndrome coronavirus 2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP*GP*C)-3')	B [auth T]	24	Severe acute respiratory syndrome coronavirus 2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCU	G [auth P]	[(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate C10 H16 N5 O6 P BLURMGIBVBRPQT-ZCFIWIBFSA-N
POP	K [auth A], O [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
ZN	I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	H [auth P], L [auth A], M [auth A], N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-15 
Deposition Author(s): Li, Z., Yu, X.

Revision History  

• Version 1.0: 2021-12-15
  Type: Initial release