ISDA: 9GDD

Deposition Date 2024-08-05

Release Date 2025-11-05

Last Version Date 2025-12-17

Entry Detail

PDB ID:

9GDD

Keywords:

TRANSCRIPTION

Title:

RNAP-TopoI complex on bubble scaffold - two-bubble configuration

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.30 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Gene (Uniprot):rpoA
Chain IDs:A, B
Chain Length:329
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7Z4 Pfam ID:PF01193, PF01000, PF03118 EC:2.7.7.6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):rpoB
Chain IDs:C
Chain Length:1342
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A8V2 Pfam ID:PF04563, PF04561, PF04565, PF10385, PF00562, PF04560 EC:2.7.7.6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Gene (Uniprot):rpoC
Chain IDs:D
Chain Length:1415
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A8T7 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998 EC:2.7.7.6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Gene (Uniprot):rpoZ
Chain IDs:E
Chain Length:91
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A800 Pfam ID:PF01192 EC:2.7.7.6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA topoisomerase 1
Gene (Uniprot):topA
Chain IDs:F
Chain Length:896
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P06612 Pfam ID:PF01751, PF01131, PF01396, PF21372, PF08272 EC:5.6.2.1

Polymer Type:polydeoxyribonucleotide
Molecule:non-template DNA strand
Chain IDs:G (auth: N)
Chain Length:53
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:RNA
Chain IDs:H (auth: R)
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:template DNA strand
Chain IDs:I (auth: T)
Chain Length:53
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation.

Vidmar, V, Borde, C, Bruno, L, Miropolskaya, N, Takacs, M, Batisse, C, Saint-Andre, C, Zhu, C, Espeli, O, Lamour, V, Weixlbaumer, A.Show

Nat.Struct.Mol.Biol. ? ? ? (2025)

PMID: 41326756 DOI: 10.1038/s41594-025-01703-5

Primary Citation of related structures

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