Download MendeleyCryo-EM structure of the Retron-Eco7 complex
Ishikawa, J., Yoneyama, K.To be published.
9KJZ | pdb_00009kjz
Cryo-EM structure of the Retron-Eco7 complex (state 3)
- PDB DOI: https://doi.org/10.2210/pdb9KJZ/pdb
- EM Map EMD-62380: EMDB EMDataResource
- Classification: RNA BINDING PROTEIN
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-11-12 Released: 2025-11-12
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.70 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RNA-directed DNA polymerase | 322 | Escherichia coli | Mutation(s): 0 Gene Names: D4M65_23810, KQO22_004355 EC: 2.7.7.49 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| AAA family ATPase | 550 | Escherichia coli | Mutation(s): 0 Gene Names: OGW11_10610 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| TIGR02646 family protein | 266 | Escherichia coli | Mutation(s): 0 Gene Names: D4M65_23820, KQO22_004357 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| msrRNA | 146 | Escherichia coli |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| msdDNA | 77 | Escherichia coli |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ADP (Subject of Investigation/LOI) Query on ADP | J [auth B], K [auth C], L [auth E] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N |  | ||
| ZN (Subject of Investigation/LOI) Query on ZN | M [auth F], N [auth G] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG (Subject of Investigation/LOI) Query on MG | O [auth H] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.70 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | Servalcat | |
| RECONSTRUCTION | cryoSPARC |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-11-12 Deposition Author(s): Ishikawa, J., Yoneyama, K., Yamashita, K., Nishimasu, H.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | 23KJ0720 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 21H05281 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 22H00403 |
Revision History (Full details and data files)
- Version 1.0: 2025-11-12
Type: Initial release
