8S7K | pdb_00008s7k

M. tuberculosis gyrase holocomplex with 150 bp DNA and gepotidacin

• PDB DOI: https://doi.org/10.2210/pdb8S7K/pdb
• NAKB: 8S7K
• EM Map EMD-19777: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-01 Released: 2025-10-08 
• Deposition Author(s): Mechaly, A., Gubellini, F., Yab, E., Willand, N., Petrella, S.
• Funding Organization(s): IdEx Universite Paris Cite, Agence Nationale de la Recherche (ANR), Fondation pour la Recherche Medicale (FRM)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

M. tuberculosis gyrase holocomplex with 150 bp DNA and gepotidacin

Gedeon, A., Yab, E., Dinut, A., Sadowski, E., Capton, E., Dreneau, A., Gioia, B., Piveteau, C., Djaout, K., Lecat, E., Wehenkel, A.M., Gubellini, F., Mechaly, A., Alzari, P.M., Deprez, B., Baulard, A., Aubry, A., Willand, N., Petrella, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 426.57 kDa 
• Atom Count: 11,314 
• Modeled Residue Count: 1,377 
• Deposited Residue Count: 3,330 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A [auth C], B [auth A]	837	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: gyrA, Rv0006, MTCY10H4.04 EC: 5.6.2.2
UniProt
Find proteins for P9WG47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG47  Go to UniProtKB:  P9WG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	C [auth B], D	678	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: gyrB, Rv0005, MTCY10H4.03 EC: 5.6.2.2
UniProt
Find proteins for P9WG45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG45  Go to UniProtKB:  P9WG45

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')	E	150	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')	F	150	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JHN (Subject of Investigation/LOI)	I [auth F]	(3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione C24 H28 N6 O3 PZFAZQUREQIODZ-LJQANCHMSA-N
MG	G [auth B], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Mechaly, A., Gubellini, F., Yab, E., Willand, N., Petrella, S.

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Funding Organization	Location	Grant Number
IdEx Universite Paris Cite	France	--
Agence Nationale de la Recherche (ANR)	France	ANR-18-IDEX-0001
Fondation pour la Recherche Medicale (FRM)	France	EQU202303016284

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release