9PJD | pdb_00009pjd

Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc substrate within a translocation complex

PDB DOI: https://doi.org/10.2210/pdb9PJD/pdb
EM Map EMD-71688: EMDB EMDataResource
NAKB: 9PJD

Classification: CHAPERONE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-13 Released: 2025-11-12
Deposition Author(s): Ghanbarpour, A., Davis, J.H., Sauer, R.T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.67 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 the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc within a translocation complex

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

To be published.

Macromolecule Content

Total Structure Weight: 610.78 kDa
Atom Count: 36,974
Modeled Residue Count: 4,749
Deposited Residue Count: 5,448
Unique protein chains: 2
Unique nucleic acid 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 ATP-binding subunit ClpX	A, B, C, D, E A, B, C, D, E, F	424	Escherichia coli	Mutation(s): 0 Gene Names: clpX
UniProt
Find proteins for C3TLS7 (Escherichia coli) Explore C3TLS7 Go to UniProtKB: C3TLS7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3TLS7
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, O, P, Q, R, S, T, U	207	Escherichia coli	Mutation(s): 0 Gene Names: clpP, lopP, b0437, JW0427 EC: 3.4.21.92
UniProt
Find proteins for P0A6G7 (Escherichia coli (strain K12)) Explore P0A6G7 Go to UniProtKB: P0A6G7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6G7
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
unidentified portion of the substrate	G	6	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth E] SDF format, chain EA [auth F] SDF format, chain V [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain V [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain V [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth C]	AA [auth D] CA [auth E] EA [auth F] V [auth A] W [auth B] AA [auth D], CA [auth E], EA [auth F], V [auth A], W [auth B], Y [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain V [auth A] Focus chain W [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain V [auth A] Focus chain W [auth B] Focus chain Y [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain FA [auth F] SDF format, chain X [auth B] SDF format, chain Z [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth C]	BA [auth D], DA [auth E], FA [auth F], X [auth B], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain X [auth B] Focus chain Z [auth C]