8YD2 | pdb_00008yd2

CryoEM structure of M. tuberculosis ClpP1P2 bound to bortezomib

• PDB DOI: https://doi.org/10.2210/pdb8YD2/pdb
• EM Map EMD-39163: EMDB EMDataResource

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


• Deposited: 2024-02-19 Released: 2025-03-19 
• Deposition Author(s): Zhou, B., Gao, Y., Zhao, H., Chen, W., He, J., Zhang, T., Xiong, X.
• Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Activation mechanism of caseinolytic chaperone-protease system in Mycobacterium tuberculosis by the anti-cancer drug bortezomib

Zhou, B., Gao, Y., Zhao, H., Chen, X., He, J., Zhang, T., Xiong, X.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Hetero 14-mer - A7B7 Pseudo Symmetry: Dihedral - D7  (Explore in 3D)
Pseudo Stoichiometry: Homo 14-mer - A14 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 279.54 kDa 
• Atom Count: 19,572 
• Modeled Residue Count: 2,506 
• Deposited Residue Count: 2,506 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 1	A, C, E, G, I, K, M	178	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: clpP1, clpP, Rv2461c, MTV008.17c EC: 3.4.21.92
UniProt
Find proteins for P9WPC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC5  Go to UniProtKB:  P9WPC5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 2	B, D, F, H, J, L, N	180	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: clpP2, Rv2460c, MTV008.16c EC: 3.4.21.92
UniProt
Find proteins for P9WPC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC3  Go to UniProtKB:  P9WPC3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BO2 (Subject of Investigation/LOI)	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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Zhou, B., Gao, Y., Zhao, H., Chen, W., He, J., Zhang, T., Xiong, X.

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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

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release