9JVZ | pdb_00009jvz

CryoEM structure of M. tuberculosis ClpP1P2 bound to bortezomib

PDB DOI: https://doi.org/10.2210/pdb9JVZ/pdb
EM Map EMD-61847: EMDB EMDataResource

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

Deposited: 2024-10-09 Released: 2025-03-19
Deposition Author(s): Zhou, B., Zhao, H., Gao, Y., Chen, W., Zhang, T., He, J., Xiong, X.
Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural Insights into Bortezomib-Induced Activation of the Caseinolytic Chaperone-Protease System in Mycobacterium tuberculosis.

Zhou, B., Gao, Y., Zhao, H., Liu, B., Zhang, H., Fang, C., Yuan, H., Wang, J., Li, Z., Zhao, Y., Huang, X., Wang, X., Oliveira, A.S.F., Spencer, J., Mulholland, A.J., Burston, S.G., Hu, J., Su, N., Chen, X., He, J., Zhang, T., Xiong, X.

(2025) Nat Commun 16: 3466-3466

PubMed: 40216758 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-58410-4
Primary Citation Related Structures:
9JVP, 9JVZ

PubMed Abstract:
The caseinolytic protease (Clp) system has recently emerged as a promising anti-tuberculosis target. The anti-cancer drug bortezomib exhibits potent anti-mycobacterial activity and binds to Mycobacterium tuberculosis (Mtb) Clp protease complexes. We determine cryo-EM structures of Mtb ClpP1P2, ClpC1P1P2 and ClpXP1P2 complexes bound to bortezomib in different conformations. Structural and biochemical data indicate that sub-stoichiometric binding by bortezomib to the protease active sites orthosterically activates the MtbClpP1P2 complex. Bortezomib activation of MtbClpP1P2 induces structural changes promoting the recruitment of the chaperone-unfoldases, MtbClpC1 or MtbClpX, facilitating holoenzyme formation. The structures of the MtbClpC1P1P2 holoenzyme indicate that MtbClpC1 motion, induced by ATP rebinding at the MtbClpC1 spiral seam, translocates the substrate. In the MtbClpXP1P2 holoenzyme structure, we identify a specialized substrate channel gating mechanism involving the MtbClpX pore-2 loop and MtbClpP2 N-terminal domains. Our results provide insights into the intricate regulation of the Mtb Clp system and suggest that bortezomib can disrupt this regulation by sub-stoichiometric binding at the Mtb Clp protease sites.

Organizational Affiliation

State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangzhou, China.

Graduate School of Guangzhou Medical University, Guangzhou Medical University-Guangzhou Institutes of Biomedicine and Health Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China.

Guangzhou National Laboratory, Guangzhou, China.

State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

University of Chinese Academy of Sciences, Beijing, China.

School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.

Guangxi Medical University Laboratory Animal Center, Nanning, China.

Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK.

School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, UK.

School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK.

Guangzhou National Laboratory, Guangzhou, China. chen_xinwen@gzlab.ac.cn.

State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China. chen_xinwen@gzlab.ac.cn.

Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China. he_jun@gibh.ac.cn.

Macromolecule Content

Total Structure Weight: 291.07 kDa
Atom Count: 19,558
Modeled Residue Count: 2,506
Deposited Residue Count: 2,611
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 1	A, B, C, D, E A, B, C, D, E, F, H	178	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: clpP1, clpP EC: 3.4.21.92
UniProt
Find proteins for P9WPC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC5 Go to UniProtKB: P9WPC5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPC5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 2	G, I, J, K, L G, I, J, K, L, M, N	195	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: clpP2 EC: 3.4.21.92
UniProt
Find proteins for P9WPC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC3 Go to UniProtKB: P9WPC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BO2 (Subject of Investigation/LOI) Query on BO2 Download Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain BA [auth N] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain V [auth H] SDF format, chain W [auth I] SDF format, chain X [auth J] SDF format, chain Y [auth K] SDF format, chain Z [auth L] MOL2 format, chain AA [auth M] MOL2 format, chain BA [auth N] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain V [auth H] MOL2 format, chain W [auth I] MOL2 format, chain X [auth J] MOL2 format, chain Y [auth K] MOL2 format, chain Z [auth L] mmCIF format, chain AA [auth M] mmCIF format, chain BA [auth N] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain V [auth H] mmCIF format, chain W [auth I] mmCIF format, chain X [auth J] mmCIF format, chain Y [auth K] mmCIF format, chain Z [auth L]	AA [auth M] BA [auth N] O [auth A] P [auth B] Q [auth C] AA [auth M], BA [auth N], O [auth A], P [auth B], Q [auth C], R [auth D], S [auth E], T [auth F], U [auth G], V [auth H], W [auth I], X [auth J], Y [auth K], Z [auth L]	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE C₁₉ H₂₅ B N₄ O₄ GXJABQQUPOEUTA-RDJZCZTQSA-N		Interactions Focus chain AA [auth M] Focus chain BA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		2021YFA1300903
Other government		2021YFA1300904
National Natural Science Foundation of China (NSFC)	China	32300152
National Natural Science Foundation of China (NSFC)	China	81973372
National Natural Science Foundation of China (NSFC)	China	32170189
National Natural Science Foundation of China (NSFC)	China	32241021
National Natural Science Foundation of China (NSFC)	China	82341085
Other government		2022A1515110505
Other government		2022M723164