9U9Y | pdb_00009u9y

Cryo-EM structure of retron Ec78 effector complex

PDB DOI: https://doi.org/10.2210/pdb9U9Y/pdb
EM Map EMD-63972: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-30 Released: 2025-12-10
Deposition Author(s): Liu, Z., Zhang, H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9U9Y

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

Literature

Cryo-EM structure of retron Ec78 effector complex

Liu, Z., Zhang, H.

To be published.

Macromolecule Content

Total Structure Weight: 150.38 kDa
Atom Count: 8,585
Modeled Residue Count: 1,062
Deposited Residue Count: 1,316
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA family ATPase	A, B	550	Escherichia coli	Mutation(s): 0 Gene Names: OGW11_10610
UniProt
Find proteins for P0DV91 (Escherichia coli) Explore P0DV91 Go to UniProtKB: P0DV91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DV91
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TIGR02646 family protein	C [auth H]	216	Escherichia coli	Mutation(s): 0 Gene Names: OGW11_10605

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20_4459
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2025-12-10
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.