Download MendeleyDNA topoisomerase I acts as supercoiling sensor for transcription elongation in E. coli
Vidmar, V., Borde, C., Bruno, L., Takacs, M., Batisse, C., Saint-Andre, C., Zhu, C., Espeli, O., Lamour, V., Weixlbaumer, A.To be published.
9GDB | pdb_00009gdb
RNAP-TopoI complex on bubble scaffold - consensus reconstruction
- PDB DOI: https://doi.org/10.2210/pdb9GDB/pdb
- EM Map EMD-51260: EMDB EMDataResource
- NAKB: 9GDB
- Classification: TRANSCRIPTION
- Organism(s): Escherichia coli, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-08-05 Released: 2025-11-05
- Funding Organization(s): Agence Nationale de la Recherche (ANR)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.80 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Models: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA-directed RNA polymerase subunit alpha | 329 | Escherichia coli | Mutation(s): 0 Gene Names: rpoA, pez, phs, sez, b3295, JW3257 EC: 2.7.7.6 |  | |
UniProt | |||||
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4 Go to UniProtKB: P0A7Z4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0A7Z4 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA-directed RNA polymerase subunit beta | 1,342 | Escherichia coli | Mutation(s): 0 Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 EC: 2.7.7.6 |  | |
UniProt | |||||
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2 Go to UniProtKB: P0A8V2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0A8V2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA-directed RNA polymerase subunit beta' | 1,415 | Escherichia coli | Mutation(s): 0 Gene Names: rpoC, tabB, b3988, JW3951 EC: 2.7.7.6 |  | |
UniProt | |||||
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7 Go to UniProtKB: P0A8T7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0A8T7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA-directed RNA polymerase subunit omega | 91 | Escherichia coli | Mutation(s): 0 Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6 |  | |
UniProt | |||||
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800 Go to UniProtKB: P0A800 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0A800 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA topoisomerase 1 | 896 | Escherichia coli | Mutation(s): 0 Gene Names: topA, supX, b1274, JW1266 EC: 5.6.2.1 |  | |
UniProt | |||||
Find proteins for P06612 (Escherichia coli (strain K12)) Explore P06612 Go to UniProtKB: P06612 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06612 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| non-template DNA strand | G [auth N] | 53 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| RNA | H [auth R] | 14 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| template DNA strand | I [auth T] | 53 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | K [auth D], L [auth D], M [auth F], N [auth F], O [auth F] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | J [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.80 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | 1.20.1 |
| MODEL REFINEMENT | Coot | 0.9.6 |
| RECONSTRUCTION | cryoSPARC |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-11-05 Deposition Author(s): Vidmar, V., Weixlbaumer, A., Lamour, V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Agence Nationale de la Recherche (ANR) | France | ANR-21-CE11-0040-01 |
| Agence Nationale de la Recherche (ANR) | France | ANR-10-INBS-05 |
Revision History (Full details and data files)
- Version 1.0: 2025-11-05
Type: Initial release
