9LBQ | pdb_00009lbq

Cryo-EM structure of the Retron-Eco8 complex

PDB DOI: https://doi.org/10.2210/pdb9LBQ/pdb
EM Map EMD-62954: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN/RNA/DNA
Organism(s): Escherichia coli
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-01-03 Released: 2026-07-01
Deposition Author(s): Zhang, J.T., Ji, C.G., Jia, N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.94 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation

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This is version 1.0 of the entry. See complete history.

Literature

Retron-Eco8 forms a heterotetramer complex to protects bacteria from phage infection

Jia, N., Zhang, J.T., Ji, C.G.

To be published.

Macromolecule Content

Total Structure Weight: 721.74 kDa
Atom Count: 37,652
Modeled Residue Count: 4,084
Deposited Residue Count: 5,128
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retron Eco8 reverse transcriptase	A, E, I, M	374	Escherichia coli	Mutation(s): 0 Gene Names: ret, ERS139198_01421, Ga0119705_103345 EC: 2.7.7.49
UniProt
Find proteins for P0DV59 (Escherichia coli) Explore P0DV59 Go to UniProtKB: P0DV59
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DV59
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retron Eco8 OLD nuclease	B, F, J, N	750	Escherichia coli	Mutation(s): 0 Gene Names: old, ERS139198_01420, Ga0119705_103344 EC: 3.1
UniProt
Find proteins for P0DV58 (Escherichia coli) Explore P0DV58 Go to UniProtKB: P0DV58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DV58
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 3
RNA (83-MER)	C, G, K, O	83	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 4
DNA (75-MER)	D, H, L, P	75	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.94 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-07-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.