8YD0 | pdb_00008yd0

CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib

PDB DOI: https://doi.org/10.2210/pdb8YD0/pdb
EM Map EMD-39161: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-02-18 Released: 2025-03-19
Deposition Author(s): Zhou, B., Zhao, H., Gao, Y., Chen, X., 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: 2.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 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

DOI: https://doi.org/10.1038/s41467-025-58410-4

Macromolecule Content

Total Structure Weight: 529.14 kDa
Atom Count: 36,135
Modeled Residue Count: 4,631
Deposited Residue Count: 4,748
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpX	A, B, C, D, E A, B, C, D, E, F	355	Mycobacterium tuberculosis H37Rv	Mutation(s): 1 Gene Names: clpX
UniProt
Find proteins for P9WPB9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPB9 Go to UniProtKB: P9WPB9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPB9
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 [auth H] H [auth I] I [auth K] J [auth L] K [auth M] G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], T [auth V]	196	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 1	M [auth O] N [auth P] O [auth Q] P [auth R] Q [auth S] M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U]	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth B] SDF format, chain V [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth B] MOL2 format, chain V [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth B] mmCIF format, chain V [auth A]	V [auth A], W [auth B], X [auth D], Y [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth D] Focus chain Y [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain BA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain BA [auth F]	BA [auth F], Z [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth F] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain Z [auth E]
BO2 (Subject of Investigation/LOI) Query on BO2 Download Ideal Coordinates CCD File SDF format, chain PA [auth V] SDF format, chain OA [auth U] SDF format, chain NA [auth T] SDF format, chain MA [auth S] SDF format, chain LA [auth R] SDF format, chain KA [auth Q] SDF format, chain JA [auth P] SDF format, chain IA [auth O] SDF format, chain HA [auth N] SDF format, chain GA [auth M] SDF format, chain FA [auth L] SDF format, chain EA [auth K] SDF format, chain DA [auth I] SDF format, chain CA [auth H] MOL2 format, chain PA [auth V] MOL2 format, chain OA [auth U] MOL2 format, chain NA [auth T] MOL2 format, chain MA [auth S] MOL2 format, chain LA [auth R] MOL2 format, chain KA [auth Q] MOL2 format, chain JA [auth P] MOL2 format, chain IA [auth O] MOL2 format, chain HA [auth N] MOL2 format, chain GA [auth M] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth K] MOL2 format, chain DA [auth I] MOL2 format, chain CA [auth H] mmCIF format, chain PA [auth V] mmCIF format, chain OA [auth U] mmCIF format, chain NA [auth T] mmCIF format, chain MA [auth S] mmCIF format, chain LA [auth R] mmCIF format, chain KA [auth Q] mmCIF format, chain JA [auth P] mmCIF format, chain IA [auth O] mmCIF format, chain HA [auth N] mmCIF format, chain GA [auth M] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth K] mmCIF format, chain DA [auth I] mmCIF format, chain CA [auth H]	CA [auth H] DA [auth I] EA [auth K] FA [auth L] GA [auth M] CA [auth H], DA [auth I], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], KA [auth Q], LA [auth R], MA [auth S], NA [auth T], OA [auth U], PA [auth V]	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE C₁₉ H₂₅ B N₄ O₄ GXJABQQUPOEUTA-RDJZCZTQSA-N		Interactions Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain OA [auth U] Focus chain PA [auth V] Interactions & Density Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain OA [auth U] Focus chain PA [auth V]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain AA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain AA [auth E] mmCIF format, chain U [auth A] mmCIF format, chain AA [auth E]	AA [auth E], U [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain U [auth A] Interactions & Density Focus chain AA [auth E] Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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