ISDA: 9GDQ

Deposition Date 2024-08-06

Release Date 2025-12-17

Last Version Date 2025-12-17

Entry Detail

PDB ID:

9GDQ

Keywords:

TRANSCRIPTION

Title:

Cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR transcription factor and ompU promoter DNA

Biological Source:

Source Organism:

Vibrio cholerae O395 (Taxon ID: 345073)
Vibrio cholerae O1 biovar El Tor str. N16961 (Taxon ID: 243277)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.10 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

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:D (auth: A), E (auth: B), G
Chain Length:330
Number of Molecules:3
Biological Source:Vibrio cholerae O395

UniProt ID:A5F572 Pfam ID:PF01193, PF01000, PF03118

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):rpoB
Chain IDs:A (auth: C)
Chain Length:1341
Number of Molecules:1
Biological Source:Vibrio cholerae O395

UniProt ID:A5F3P5 Pfam ID:PF04563, PF04561, PF04565, PF10385, PF00562, PF04560

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Gene (Uniprot):rpoC
Chain IDs:B (auth: D)
Chain Length:1401
Number of Molecules:1
Biological Source:Vibrio cholerae O395

UniProt ID:A5F3P6 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Gene (Uniprot):rpoZ
Chain IDs:C (auth: E)
Chain Length:90
Number of Molecules:1
Biological Source:Vibrio cholerae O395

UniProt ID:A5F4S8 Pfam ID:PF01192

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA polymerase sigma factor RpoD
Gene (Uniprot):rpoD
Chain IDs:F
Chain Length:621
Number of Molecules:1
Biological Source:Vibrio cholerae O395

UniProt ID:A0A0H3AJ64 Pfam ID:PF03979, PF00140, PF04546, PF04542, PF04539, PF04545

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cholera toxin transcriptional activator
Gene (Uniprot):toxR
Chain IDs:H (auth: K), K (auth: H)
Chain Length:110
Number of Molecules:2
Biological Source:Vibrio cholerae O1 biovar El Tor str. N16961

UniProt ID:P15795 Pfam ID:PF00486

Polymer Type:polydeoxyribonucleotide
Molecule:ompU promoter non-template DNA strand
Chain IDs:J (auth: N)
Chain Length:69
Number of Molecules:1
Biological Source:Vibrio cholerae O395

Polymer Type:polydeoxyribonucleotide
Molecule:ompU promoter template DNA strand
Chain IDs:I (auth: T)
Chain Length:69
Number of Molecules:1
Biological Source:Vibrio cholerae O395

Ligand Molecules

Primary Citation

Structures of Vibrio cholerae transcription complexes reveal how ToxR and TcpP recruit the RNA polymerase and activate virulence genes

Alcaide-Jimenez, A, Canals, A, Baudin, F, Machon, C, Fabrega-Ferrer, M, Bantysh, O, Perez-Luque, R, Murciano, B, Mohammad, A.A, Rowse, M.J, Ferracciolo, J.M, Krukonis, E.S, Muller, C.W, Coll, M.Show

Science Advances ? ? ? (2025)

Primary Citation of related structures

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