Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A1BCD 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 177.13 kDa 
• Atom Count: 10692 
• Residue Count: 1288 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

7C2K

COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex

• DOI: 10.2210/pdb7C2K/pdb
• EMDataResource: EMD-30275

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Foot-and-mouth disease virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-07 Released: 2020-06-03 
• Deposition Author(s): Wang, Q., Gao, Y., Ji, W., Mu, A., Rao, Z.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.

Wang, Q., Wu, J., Wang, H., Gao, Y., Liu, Q., Mu, A., Ji, W., Yan, L., Zhu, Y., Zhu, C., Fang, X., Yang, X., Huang, Y., Gao, H., Liu, F., Ge, J., Sun, Q., Yang, X., Xu, W., Liu, Z., Yang, H., Lou, Z., Jiang, B., Guddat, L.W., Gong, P., Rao, Z.

(2020) Cell 

• PubMed: 32526208 
• DOI: 10.1016/j.cell.2020.05.034
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Nucleotide analog inhibitors, including broad-spectrum remdesivir and favipiravir, have shown promise in in vitro assays and some clinical studies for COVID-19 treatment, this despite an incomplete mechanistic understanding of the viral RNA-dependent RNA polymerase nsp12 drug interactions. Here, we examine the molecular basis of SARS-CoV-2 RNA replication by determining the cryo-EM structures of the stalled pre- and post- translocated polymerase complexes. Compared with the apo complex, the structures show notable structural rearrangements happening to nsp12 and its co-factors nsp7 and nsp8 to accommodate the nucleic acid, whereas there are highly conserved residues in nsp12, positioning the template and primer for an in-line attack on the incoming nucleotide. Furthermore, we investigate the inhibition mechanism of the triphosphate metabolite of remdesivir through structural and kinetic analyses. A transition model from the nsp7-nsp8 hexadecameric primase complex to the nsp12-nsp7-nsp8 polymerase complex is also proposed to provide clues for the understanding of the coronavirus transcription and replication machinery.

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Organizational Affiliation: 

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RNA-directed RNA polymerase	A	944	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.7.7.48 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Non-structural protein 8	B, D	200	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Go to UniProtKB:  P0DTD1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Non-structural protein 7	C	85	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Go to UniProtKB:  P0DTD1

Entity ID: 4
Molecule	Chains	Length	Organism
RNA (29-MER)	F	29	Foot-and-mouth disease virus

Entity ID: 5
Molecule	Chains	Length	Organism
RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*G)-3')	G	18	Foot-and-mouth disease virus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-05-07 
• Released Date: 2020-06-03 
Deposition Author(s): Wang, Q., Gao, Y., Ji, W., Mu, A., Rao, Z.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFC0840300
Ministry of Science and Technology (MoST, China)	China	2020YFA0707500
Ministry of Science and Technology (MoST, China)	China	2018YFA0507200
Chinese Academy of Sciences	China	XDB08020200
National Natural Science Foundation of China (NSFC)	China	81520108019
National Natural Science Foundation of China (NSFC)	China	813300237
National Natural Science Foundation of China (NSFC)	China	32041007

Revision History 

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-06-24
  Changes: Database references