9PIO | pdb_00009pio

Cryo-EM structure of the ClpXP AAA+ protease bound to lambdaO-tagged Arc in a recognition complex

PDB DOI: https://doi.org/10.2210/pdb9PIO/pdb
EM Map EMD-71674: EMDB EMDataResource

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

Deposited: 2025-07-10 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: 2.61 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of substrate-free full-length ClpX.ClpP complex

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

To be published.

Macromolecule Content

Total Structure Weight: 619.02 kDa
Atom Count: 36,436
Modeled Residue Count: 4,675
Deposited Residue Count: 5,521
Unique protein chains: 3

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3TLS7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Arc family DNA-binding protein	G	79	Escherichia coli	Mutation(s): 0 Gene Names: G4A38_03820, G4A47_21235, GP965_26270, GP979_03530, NCTC10082_04398, QDW62_07975, R8G00_06260
UniProt
Find proteins for A0A1Y5CGZ0 (Escherichia coli) Explore A0A1Y5CGZ0 Go to UniProtKB: A0A1Y5CGZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1Y5CGZ0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6G7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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