9GDQ | pdb_00009gdq

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

• PDB DOI: https://doi.org/10.2210/pdb9GDQ/pdb
• EM Map EMD-51275: EMDB EMDataResource
• NAKB: 9GDQ

• Classification: TRANSCRIPTION
• Organism(s): Vibrio cholerae O395, Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-06 Released: 2025-12-17 
• Deposition Author(s): Alcaide-Jimenez, A., Baudin, F., Canals, A., Machon, C., Murciano, B., Fabrega-Ferrer, M., Bantysh, O., Perez-Luque, R., Krukonis, E.S., Muller, C.W., Coll, M.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN), Generalitat de Catalunya

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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.

(2025) Science Advances 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C1D1E1F1G1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 563.51 kDa 
• Atom Count: 32,619 
• Modeled Residue Count: 3,922 
• Deposited Residue Count: 4,801 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	A [auth C]	1,341	Vibrio cholerae O395	Mutation(s): 0  Gene Names: rpoB, VC0395_A2730, VC395_0371 EC: 2.7.7.6
UniProt
Find proteins for A5F3P5 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F3P5  Go to UniProtKB:  A5F3P5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	B [auth D]	1,401	Vibrio cholerae O395	Mutation(s): 0  Gene Names: rpoC, VC0395_A2731, VC395_0372 EC: 2.7.7.6
UniProt
Find proteins for A5F3P6 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F3P6  Go to UniProtKB:  A5F3P6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	C [auth E]	90	Vibrio cholerae O395	Mutation(s): 0  Gene Names: rpoZ, VC0395_A2281, VC395_2821 EC: 2.7.7.6
UniProt
Find proteins for A5F4S8 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F4S8  Go to UniProtKB:  A5F4S8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	D [auth A], E [auth B], G	330	Vibrio cholerae O395	Mutation(s): 0  Gene Names: rpoA, VC0395_A2149, VC395_2684 EC: 2.7.7.6
UniProt
Find proteins for A5F572 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F572  Go to UniProtKB:  A5F572

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor RpoD	F	621	Vibrio cholerae O395	Mutation(s): 0  Gene Names: rpoD, VC0395_A0044
UniProt
Find proteins for A0A0H3AJ64 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AJ64  Go to UniProtKB:  A0A0H3AJ64

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera toxin transcriptional activator	H [auth K], K [auth H]	110	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: toxR, VC_0984
UniProt
Find proteins for P15795 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P15795  Go to UniProtKB:  P15795

Entity ID: 7
Molecule	Chains	Length	Organism	Image
ompU promoter template DNA strand	I [auth T]	69	Vibrio cholerae O395

Entity ID: 8
Molecule	Chains	Length	Organism	Image
ompU promoter non-template DNA strand	J [auth N]	69	Vibrio cholerae O395

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	L [auth D], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Alcaide-Jimenez, A., Baudin, F., Canals, A., Machon, C., Murciano, B., Fabrega-Ferrer, M., Bantysh, O., Perez-Luque, R., Krukonis, E.S., Muller, C.W., Coll, M.

---

Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2020-12141GB-100
Generalitat de Catalunya	Spain	2021SGR00423

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release