9DW3 | pdb_00009dw3

Human mitochondrial ClpP in complex with Bortezomib

PDB DOI: https://doi.org/10.2210/pdb9DW3/pdb
EM Map EMD-47234: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-08 Released: 2025-10-15
Deposition Author(s): Chen, W.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Assembly and proteolytic activation human ClpXP defined by cryo-EM

Chen, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 342.68 kDa
Atom Count: 19,936
Modeled Residue Count: 2,534
Deposited Residue Count: 3,080
Unique protein chains: 1

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, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	220	Homo sapiens	Mutation(s): 0 Gene Names: CLPP EC: 3.4.21.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q16740 (Homo sapiens) Explore Q16740 Go to UniProtKB: Q16740
PHAROS: Q16740 GTEx: ENSG00000125656
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16740
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: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Chen, W.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10OD032467
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS095892