7OYG

Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase

• PDB DOI: https://doi.org/10.2210/pdb7OYG/pdb
• EM Map EMD-13116: EMDB EMDataResource
• NAKB: 7OYG

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


• Deposited: 2021-06-24 Released: 2021-08-25 
• Deposition Author(s): Jochheim, F.A., Tegunov, D., Hillen, H.S., Schmitzova, J., Kokic, G., Dienemann, C., Cramer, P.
• Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The structure of a dimeric form of SARS-CoV-2 polymerase

Jochheim, F.A., Tegunov, D., Hillen, H.S., Schmitzova, J., Kokic, G., Dienemann, C., Cramer, P.

(2021) Communications Biology 4: 999

• DOI: https://doi.org/10.1038/s42003-021-02529-9

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 323.65 kDa 
• Atom Count: 16,274 
• Modelled Residue Count: 1,958 
• Deposited Residue Count: 2,588 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 RNA-dependent RNA polymerase (nsp12)	A, F [auth D]	935	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
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
SARS-CoV-2 nsp8	B, G [auth E]	201	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 nsp7	C, H [auth F]	86	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3')	D [auth P], I [auth G]	15	Severe acute respiratory syndrome coronavirus 2

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3')	E [auth T], J [auth H]	57	Severe acute respiratory syndrome coronavirus 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	K [auth A], L [auth A], M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Jochheim, F.A., Tegunov, D., Hillen, H.S., Schmitzova, J., Kokic, G., Dienemann, C., Cramer, P.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	Germany	882357
German Research Foundation (DFG)	Germany	EXC 2067/1 39072994
German Research Foundation (DFG)	Germany	SFB860
German Research Foundation (DFG)	Germany	SPP2191
German Research Foundation (DFG)	Germany	EXC 2067/1 39072994
German Research Foundation (DFG)	Germany	SFB1190
German Research Foundation (DFG)	Germany	FOR2848

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release
  
• Version 1.1: 2021-09-01
  Changes: Database references