8YD1 | pdb_00008yd1

CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 1

PDB DOI: https://doi.org/10.2210/pdb8YD1/pdb
EM Map EMD-39162: EMDB EMDataResource

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

Deposited: 2024-02-19 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: 2.81 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: 727.4 kDa
Atom Count: 43,440
Modeled Residue Count: 5,512
Deposited Residue Count: 6,479
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpC1	A, B, C, D, E A, B, C, D, E, F	657	Mycobacterium tuberculosis H37Rv	Mutation(s): 3 Gene Names: clpC1
UniProt
Find proteins for P9WPC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC9 Go to UniProtKB: P9WPC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPC9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 2	G, H, I, J, K G, H, I, J, K, L, M	181	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPC3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 1	N, O, P, Q, R N, O, P, Q, R, S, T	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPC5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-casein	U [auth a]	24	Bos grunniens	Mutation(s): 0
UniProt
Find proteins for P02666 (Bos taurus) Explore P02666 Go to UniProtKB: P02666
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02666
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 A] SDF format, chain W [auth A] SDF format, chain JA [auth D] SDF format, chain GA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain W [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain W [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] CA [auth B] DA [auth C] GA [auth C] JA [auth D] BA [auth B], CA [auth B], DA [auth C], GA [auth C], JA [auth D], W [auth A], Y [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth C] Focus chain GA [auth C] Focus chain JA [auth D] Focus chain W [auth A] Focus chain Y [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth C] Focus chain GA [auth C] Focus chain JA [auth D] Focus chain W [auth A] Focus chain Y [auth A]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain LA [auth F] SDF format, chain KA [auth E] SDF format, chain HA [auth D] MOL2 format, chain LA [auth F] MOL2 format, chain KA [auth E] MOL2 format, chain HA [auth D] mmCIF format, chain LA [auth F] mmCIF format, chain KA [auth E] mmCIF format, chain HA [auth D]	HA [auth D], KA [auth E], LA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain HA [auth D] Focus chain KA [auth E] Focus chain LA [auth F] Interactions & Density Focus chain HA [auth D] Focus chain KA [auth E] Focus chain LA [auth F]
BO2 (Subject of Investigation/LOI) Query on BO2 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth T] SDF format, chain YA [auth S] SDF format, chain XA [auth R] SDF format, chain WA [auth Q] SDF format, chain VA [auth P] SDF format, chain UA [auth O] SDF format, chain TA [auth N] SDF format, chain SA [auth M] SDF format, chain RA [auth L] SDF format, chain QA [auth K] SDF format, chain PA [auth J] SDF format, chain OA [auth I] SDF format, chain NA [auth H] SDF format, chain MA [auth G] MOL2 format, chain ZA [auth T] MOL2 format, chain YA [auth S] MOL2 format, chain XA [auth R] MOL2 format, chain WA [auth Q] MOL2 format, chain VA [auth P] MOL2 format, chain UA [auth O] MOL2 format, chain TA [auth N] MOL2 format, chain SA [auth M] MOL2 format, chain RA [auth L] MOL2 format, chain QA [auth K] MOL2 format, chain PA [auth J] MOL2 format, chain OA [auth I] MOL2 format, chain NA [auth H] MOL2 format, chain MA [auth G] mmCIF format, chain ZA [auth T] mmCIF format, chain YA [auth S] mmCIF format, chain XA [auth R] mmCIF format, chain WA [auth Q] mmCIF format, chain VA [auth P] mmCIF format, chain UA [auth O] mmCIF format, chain TA [auth N] mmCIF format, chain SA [auth M] mmCIF format, chain RA [auth L] mmCIF format, chain QA [auth K] mmCIF format, chain PA [auth J] mmCIF format, chain OA [auth I] mmCIF format, chain NA [auth H] mmCIF format, chain MA [auth G]	MA [auth G] NA [auth H] OA [auth I] PA [auth J] QA [auth K] MA [auth G], NA [auth H], OA [auth I], PA [auth J], QA [auth K], RA [auth L], SA [auth M], TA [auth N], UA [auth O], VA [auth P], WA [auth Q], XA [auth R], YA [auth S], ZA [auth T]	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE C₁₉ H₂₅ B N₄ O₄ GXJABQQUPOEUTA-RDJZCZTQSA-N		Interactions Focus chain MA [auth G] Focus chain NA [auth H] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth K] Focus chain RA [auth L] Focus chain SA [auth M] Focus chain TA [auth N] Focus chain UA [auth O] Focus chain VA [auth P] Focus chain WA [auth Q] Focus chain XA [auth R] Focus chain YA [auth S] Focus chain ZA [auth T] Interactions & Density Focus chain MA [auth G] Focus chain NA [auth H] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth K] Focus chain RA [auth L] Focus chain SA [auth M] Focus chain TA [auth N] Focus chain UA [auth O] Focus chain VA [auth P] Focus chain WA [auth Q] Focus chain XA [auth R] Focus chain YA [auth S] Focus chain ZA [auth T]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain X [auth A] SDF format, chain V [auth A] SDF format, chain IA [auth D] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth A] MOL2 format, chain V [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth A] mmCIF format, chain V [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] EA [auth C] FA [auth C] IA [auth D] V [auth A] AA [auth B], EA [auth C], FA [auth C], IA [auth D], V [auth A], X [auth A], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain V [auth A] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain V [auth A] Focus chain X [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

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