9NDJ | pdb_00009ndj

Cryo-EM structure of the endogenous ClpP1/ClpP2 heterocomplex from Pseudomonas aeruginosa bound to the AAA+ ClpX unfoldase.

PDB DOI: https://doi.org/10.2210/pdb9NDJ/pdb
EM Map EMD-49274: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Pseudomonas aeruginosa, Escherichia coli
Expression System: Escherichia coli, Pseudomonas aeruginosa
Mutation(s): No

Deposited: 2025-02-18 Released: 2025-10-01
Deposition Author(s): Ghanbarpour, A., Zhang, J.J., Baker, T.A., Davis, J.H., Sauer, R.T.
Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of ClpX from Pseudomonas aeruginosa

Ghanbarpour, A., Sauer, R.T., Davis, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 612.64 kDa
Atom Count: 36,725
Modeled Residue Count: 4,706
Deposited Residue Count: 5,515
Unique protein chains: 4

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 [auth F] B [auth A] C [auth B] D [auth C] E [auth D] A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	426	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: clpX, ALP65_100029
UniProt
Find proteins for Q9I2U0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I2U0 Go to UniProtKB: Q9I2U0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I2U0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown substrate	G	5	Escherichia coli	Mutation(s): 0
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	H, I, J, K, L H, I, J, K, L, M, N	213	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: clpP_4, clpP, ALP65_02974, CAZ10_25705, GNQ48_00520, GUL26_19790, IPC1295_05810, PAERUG_P19_London_7_VIM_2_05_10_05994 EC: 3.4.21.92
UniProt
Find proteins for Q9I2U1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I2U1 Go to UniProtKB: Q9I2U1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I2U1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	O [auth P] P [auth Q] Q [auth R] R [auth S] S [auth T] O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T], T [auth U], U [auth V]	209	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: clpP, ALP65_00001 EC: 3.4.21.92
UniProt
Find proteins for Q9HYR9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYR9 Go to UniProtKB: Q9HYR9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HYR9
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 X [auth A] SDF format, chain W [auth F] SDF format, chain CA [auth C] SDF format, chain AA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain W [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain W [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain AA [auth B]	AA [auth B], CA [auth C], W [auth F], X [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth C] Focus chain W [auth F] Focus chain X [auth A] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth C] Focus chain W [auth F] Focus chain X [auth A]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain EA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain EA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain EA [auth D]	EA [auth D], GA [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain EA [auth D] Focus chain GA [auth E] Interactions & Density Focus chain EA [auth D] Focus chain GA [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain V [auth F] SDF format, chain FA [auth E] SDF format, chain DA [auth D] SDF format, chain BA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth F] MOL2 format, chain FA [auth E] MOL2 format, chain DA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth F] mmCIF format, chain FA [auth E] mmCIF format, chain DA [auth D] mmCIF format, chain BA [auth C]	BA [auth C] DA [auth D] FA [auth E] V [auth F] Y [auth B] BA [auth C], DA [auth D], FA [auth E], V [auth F], Y [auth B], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain V [auth F] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain V [auth F] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.14_3260:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	R01-GM144542
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM141517
National Science Foundation (NSF, United States)	United States	2046778