9IMM | pdb_00009imm

SARS-CoV-2 Replication-Transcription Complex has a dimer architecture (local dRTC) in post-capping state

• PDB DOI: https://doi.org/10.2210/pdb9IMM/pdb
• EM Map EMD-60693: EMDB EMDataResource
• NAKB: 9IMM

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


• Deposited: 2024-07-03 Released: 2025-08-20 
• Deposition Author(s): Yan, L.M., Rao, Z.H., Lou, Z.Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), Major Project of Guangzhou National Laboratory, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for the concurrence of template recycling and RNA capping in SARS-CoV-2

Yan, L.M., Rao, Z.H., Lou, Z.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B2C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A2B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 344.53 kDa 
• Atom Count: 22,938 
• Modeled Residue Count: 2,757 
• Deposited Residue Count: 2,844 
• Unique protein chains: 5
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase nsp12	A	932	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.7.7.48 (PDB Primary Data), 2.7.7.50 (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
Non-structural protein 8	B, D	198	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	Sequence Length	Organism	Details	Image
Non-structural protein 7	C	83	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase nsp13	E, F	601	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
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
Viral protein genome-linked nsp9	G	113	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: 6
Molecule	Chains	Length	Organism	Image
RNA (5'-D(*(ATP))-R(P*UP*UP*AP*AP*AP*GP*GP*UP*U)-3')	H [auth O]	10	Severe acute respiratory syndrome coronavirus 2

Entity ID: 7
Molecule	Chains	Length	Organism	Image
RNA (40-MER)	I [auth P]	40	Severe acute respiratory syndrome coronavirus 2

Entity ID: 8
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*CP*CP*UP*UP*CP*CP*C)-3')	J [auth Q]	9	Severe acute respiratory syndrome coronavirus 2

Entity ID: 9
Molecule	Chains	Length	Organism	Image
RNA (59-MER)	K [auth R]	59	Severe acute respiratory syndrome coronavirus 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	L [auth A], M [auth A], N [auth E], O [auth E], P [auth E], Q [auth F], R [auth F], S [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Yan, L.M., Rao, Z.H., Lou, Z.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2024YFC2607304
Major Project of Guangzhou National Laboratory	China	GZNL2023A01008
National Natural Science Foundation of China (NSFC)	China	82341073
National Natural Science Foundation of China (NSFC)	China	32371258

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release