9YKX | pdb_00009ykx

Un-crosslinked hClpX

PDB DOI: https://doi.org/10.2210/pdb9YKX/pdb
EM Map EMD-71595: EMDB EMDataResource

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

Deposited: 2025-10-08 Released: 2026-03-04
Deposition Author(s): Chen, W.C.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/Office of the Director, National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.40 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

Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation

Chen, W., Lander, G.C., Yang, J.

(2026) Nat Commun 17: 1064

DOI: https://doi.org/10.1038/s41467-025-67010-1

Macromolecule Content

Total Structure Weight: 383.97 kDa
Atom Count: 13,558
Modeled Residue Count: 1,829
Deposited Residue Count: 3,462
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 clpX-like chaperone, mitochondrial	A, B, C, D, E A, B, C, D, E, F	577	Homo sapiens	Mutation(s): 0 Gene Names: CLPX EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for O76031 (Homo sapiens) Explore O76031 Go to UniProtKB: O76031
PHAROS: O76031 GTEx: ENSG00000166855
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O76031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 K [auth C] SDF format, chain M [auth D] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B], K [auth C], M [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain O [auth E] MOL2 format, chain O [auth E] mmCIF format, chain O [auth E]	O [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth E] Interactions & Density Focus chain O [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	G [auth A], I [auth B], L [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.0
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Chen, W.C.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--
National Institutes of Health/Office of the Director	United States	S10 OD032467
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS095892