9L7P | pdb_00009l7p

Cryo-EM structure of retron Ec78 system complex

• PDB DOI: https://doi.org/10.2210/pdb9L7P/pdb
• EM Map EMD-62876: EMDB EMDataResource
• NAKB: 9L7P

• Classification: ANTIVIRAL PROTEIN/DNA/RNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-26 Released: 2025-12-10 
• Deposition Author(s): Liu, Z., Zhang, H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of retron Ec78 system complex

Liu, Z., Zhang, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A2B2C2D1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 488.1 kDa 
• Atom Count: 24,962 
• Modeled Residue Count: 2,836 
• Deposited Residue Count: 3,482 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA family ATPase	A, B, C, D	550	Escherichia coli	Mutation(s): 0  Gene Names: OGW11_10610

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retron St85 family RNA-directed DNA polymerase	E, F	311	Escherichia coli	Mutation(s): 0  Gene Names: OGW11_10615

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TIGR02646 family protein	G [auth H]	216	Escherichia coli	Mutation(s): 0  Gene Names: OGW11_10605

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (40-MER)	H [auth I], J [auth K]	144	Escherichia coli

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (73-MER)	I [auth J], K [auth L]	78	Escherichia coli

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	L [auth B], M [auth C], N [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN	O [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	P [auth I], Q [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Liu, Z., Zhang, H.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release