8RCX | pdb_00008rcx

Crystal structure of the Mycobacterium tuberculosis regulator VirS (N-terminal fragment 4-208) in complex with the drug candidate alpibectir

• PDB DOI: https://doi.org/10.2210/pdb8RCX/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-07 Released: 2025-10-29 
• Deposition Author(s): Edoo, Z., Frita, R., Grosse, C., Bourotte, M., Moune, M., Antoine, R., Trebosc, V., Schellhorn, B., Dreneau, A., Hofmann, L., Kemmer, C., Lociuro, S., Dale, G.E., Jung, F., Perez-Herran, E., Mendoza, A., Rebollo Lopez, M.J., Ghidelli-Disse, S., Drewes, G., Mathys, V., Soetaert, K., Megalizzi, V., Wintjens, R., Barros Aguirre, D., Remuinan, M.D., Gitzinger, M., Deprez, B., Willand, N., Pieren, M., Baulard, A.R.
• Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS), Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.204 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 

Starting Model: in silico

Literature

Clinical candidate alpibectir rejuvenates ethionamide for treating tuberculosis

Edoo, Z., Frita, R., Grosse, C., Bourotte, M., Moune, M., Antoine, R., Trebosc, V., Schellhorn, B., Dreneau, A., Hofmann, L., Kemmer, C., Lociuro, S., Dale, G.E., Jung, F., Perez-Herran, E., Mendoza, A., Rebollo Lopez, M.J., Ghidelli-Disse, S., Drewes, G., Mathys, V., Soetaert, K., Megalizzi, V., Wintjens, R., Barros Aguirre, D., Remuinan, M.D., Gitzinger, M., Deprez, B., Willand, N., Pieren, M., Baulard, A.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.81 kDa 
• Atom Count: 3,492 
• Modeled Residue Count: 410 
• Deposited Residue Count: 806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator VirS	A, B	403	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: virS
UniProt
Find proteins for P9WMJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMJ3  Go to UniProtKB:  P9WMJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YPQ (Subject of Investigation/LOI)	C [auth A], D [auth B]	4,4,4-tris(fluoranyl)-1-[3-(trifluoromethyl)-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl]butan-1-one C12 H14 F6 N2 O2 ZEAVKHMQTZBUND-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.204 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.313	α = 90
b = 115.313	β = 90
c = 70.713	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Edoo, Z., Frita, R., Grosse, C., Bourotte, M., Moune, M., Antoine, R., Trebosc, V., Schellhorn, B., Dreneau, A., Hofmann, L., Kemmer, C., Lociuro, S., Dale, G.E., Jung, F., Perez-Herran, E., Mendoza, A., Rebollo Lopez, M.J., Ghidelli-Disse, S., Drewes, G., Mathys, V., Soetaert, K., Megalizzi, V., Wintjens, R., Barros Aguirre, D., Remuinan, M.D., Gitzinger, M., Deprez, B., Willand, N., Pieren, M., Baulard, A.R.

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Funding Organization	Location	Grant Number
Fonds National de la Recherche Scientifique (FNRS)	Belgium	CR40003580
Agence Nationale de la Recherche (ANR)	France	ANR-20-PAMR-0005

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release