9DVY | pdb_00009dvy

Human mitochondrial ClpX with endogenous substrate

PDB DOI: https://doi.org/10.2210/pdb9DVY/pdb
EM Map EMD-47226: EMDB EMDataResource

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

Deposited: 2024-10-08 Released: 2025-10-15
Deposition Author(s): Chen, W.C.
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: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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., Yang, J., Lander, G.C.

To be published.

Macromolecule Content

Total Structure Weight: 314.68 kDa
Atom Count: 14,432
Modeled Residue Count: 1,960
Deposited Residue Count: 2,814
Unique protein chains: 2

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-like, mitochondrial	A, B, C, D, E A, B, C, D, E, F	467	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unidentified endogenous substrate	G	12	Escherichia coli	Mutation(s): 0
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 B] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth A]	I [auth A], K [auth B], M [auth C], O [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain P [auth E] MOL2 format, chain P [auth E] mmCIF format, chain P [auth E]	P [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain P [auth E] Interactions & Density Focus chain P [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B], L [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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.C.

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