9BBJ | pdb_00009bbj

M. tuberculosis ClpC1-NTD complexed with a click chemistry analog of Rufomycin

• PDB DOI: https://doi.org/10.2210/pdb9BBJ/pdb

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


• Deposited: 2024-04-05 Released: 2025-12-10 
• Deposition Author(s): Abad-Zapatero, C., Ratia, K.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.294 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.264 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Unique Interactions of Novel Rufomycin "Click Chemistry" Analogs with Mtb ClpC1 and Implications.

Ratia, K., Jin, S., Abad-Zapatero, C., Shetye, G.S., Demissie, R., Qader, M., Beautrait, A., Nikolic, D.S., Wolf, N.M., Rubin, E.J., Krandor, O., Serbina, N., Li, G., Pauli, G.F., Klein, L.L., Cho, S., Franzblau, S.G., Fotouhi, N., Kaneko, T., Lee, H.

(2025) J Med Chem 68: 26298-26310

• PubMed: 41384615 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c02416
• Primary Citation of Related Structures:  
  9BBJ


• PubMed Abstract: 
  

  Disrupting protein homeostasis in Mycobacterium tuberculosis ( Mtb ) by targeting the ClpC1P1P2 proteolytic complex is a promising anti-TB strategy. We synthesized conformationally constrained monomeric and dimeric rufomycin 4/6 (RUF) analogs via click chemistry. While most monomeric analogs were inactive, dimeric analogs displayed potent anti- Mtb activity. Surface plasmon resonance revealed tight, slow-dissociating binding of dimers to the ClpC1 N-terminal domain (ClpC1 _NTD ), indicating prolonged residency time. X-ray crystallography and size exclusion chromatography demonstrated that dimeric analogs induce NTD dimerization, likely shifting the equilibrium toward enzymatically active hexamers rather than inactive decamers. Dimers enhanced ATPase activity over 10-fold, surpassing that of ecumicin (8-fold) and far exceeding RUF (<2-fold). Notably, our dimers bind two NTDs per molecule (1:2), contrasting with RUF (1:1) and ecumicin (2:1), suggesting a distinct activation mechanism. These RUF-based click chemistry dimers represent potent ClpC1 modulators with extended residency and novel stoichiometry, offering promising tools for studying protein degradation.

---

Organizational Affiliation: 
• Biophysics Core at Research Resource CenterUniversity of Illinois at Chicago, Chicago, Illinois 60607, United States.
Schrödinger Inc., New York, New York 10036, United States.
Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States.
The Global Alliance for TB Drug Development Inc., New York, New York 10005, United States.
Institute for Tuberculosis Research and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States.
Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, College of Pharmacy, and Biophysics Core at Research Resource Center, University of Illinois at Chicago, Chicago, Illinois 60607-60612, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.49 kDa 
• Atom Count: 1,191 
• Modeled Residue Count: 152 
• Deposited Residue Count: 165 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpC1	A	158	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: clpC1, Rv3596c, MTCY07H7B.26
UniProt
Find proteins for P9WPC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC9  Go to UniProtKB:  P9WPC9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Click chemistry analog of Rufomycin	B	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1AL8	B	L-PEPTIDE LINKING	C16 H20 N2 O2		TRP
A1AMB	B	L-PEPTIDE LINKING	C5 H8 N4 O2		ALA
A1AMC	B	L-PEPTIDE LINKING	C6 H13 N O3		ALA
MLE	B	L-PEPTIDE LINKING	C7 H15 N O2		LEU
NLE	B	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.294 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.264 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.97	α = 90
b = 57.97	β = 90
c = 131.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Abad-Zapatero, C., Ratia, K.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI142735

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release
  
• Version 1.1: 2025-12-24
  Changes: Database references
• Version 1.2: 2025-12-31
  Changes: Database references
• Version 1.3: 2026-01-07
  Changes: Database references