9DIN | pdb_00009din

Structure of ClpC1 N-terminal Domain complexed with semi-synthetic Rufomycin analog

• PDB DOI: https://doi.org/10.2210/pdb9DIN/pdb

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


• Deposited: 2024-09-05 Released: 2025-04-16 
• Deposition Author(s): Abad-Zapatero, C., Wolf, N.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Analysis of Semisynthetic Anti-TB Rufomycin Analogues.

Zhou, B., Shetye, G., Klein, L.L., Wolf, N.M., Lee, H., McAlpine, J.B., Harris, G., Chen, S.N., Suh, J.W., Cho, S.H., Franzblau, S.G., Abad-Zapatero, C., Pauli, G.F.

(2025) J Nat Prod 88: 907-925

• PubMed: 40126472 
• DOI: https://doi.org/10.1021/acs.jnatprod.4c01266
• Primary Citation of Related Structures:  
  9DIN


• PubMed Abstract: 
  

  This study employed structural information from cocrystals of rufomycin 4 ( 1a ) and caseinolytic protein C1 (ClpC1)-NTD-wt to guide design and semisynthesis of rufomycin analogues, evaluate their antituberculosis (TB) biological profiles, and establish structure-activity relationships (SAR). Covering three regions of interest (ROIs, A-C) as modification sites, 14 of the 30 semisynthetic analogues ( 2 - 31 ) showed similar or improved MICs relative to the main natural precursors, rufomycins 4/6 ( 1a/b ). Compounds 5 and 27 exhibited up to 10-fold enhanced potency against Mycobacterium tuberculosis ( Mtb ) in vitro, with MIC values of 1.9 and 1.4 nM, respectively. Evaluation of ClpC1-binding properties used existing ClpC1-NTD complexes with rufomycin 4 (PDB: 6cn8) and ecumicin (PDB: 6pbs) as references. The newly reported X-ray ClpC1-NTD cocrystal structure of 11 (syn. But4-Cl) revealed significant conformational effects involving the side chains of certain amino acids of the heptapeptide and confirmed the importance of ROIs A-C for medicinal chemistry efforts. Observed interactions of the N -terminal tail of ClpC1 with the rufomycin analogues vs ecumicin explains their different modes of inactivating the ClpC1/P1/P2 homeostatic machinery. Collectively, the observations inform further SAR optimization strategies for the rufomycin class of antibiotics and complement our understanding of their mode of action.

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Organizational Affiliation: 
• Myongji Bioefficacy Research Center, Myongji University, Myongji-Ro 116, Yongin, Gyeonggi-Do 17058, Republic of Korea.
Microbiohealthcare Co., Ltd., Myongji-Ro 116, Yongin, Gyeonggi-Do 17058, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 18.81 kDa 
• Atom Count: 1,258 
• Modeled Residue Count: 151 
• 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
Rufomycin analog	B [auth C]	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY (Subject of Investigation/LOI)	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1A5S	B [auth C]	L-PEPTIDE LINKING	C16 H21 Cl N2 O3		TRP
A1A5T	B [auth C]	L-PEPTIDE LINKING	C11 H23 N O3		LEU
MLE	B [auth C]	L-PEPTIDE LINKING	C7 H15 N O2		LEU
NIY	B [auth C]	L-PEPTIDE LINKING	C9 H10 N2 O5		TYR
NLE	B [auth C]	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002569	B [auth C]	Rufomycin analog	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.96	α = 90
b = 58.16	β = 90
c = 60.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Abad-Zapatero, C., Wolf, N.M.

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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: 2025-04-16
  Type: Initial release
  
• Version 1.1: 2025-05-07
  Changes: Database references