9OTX | pdb_00009otx

Cryo-EM structure of the Substrate-bound clpXP complex (clpX harbors the Q208A mutation in subunits B, D, and F), Class-III

PDB DOI: https://doi.org/10.2210/pdb9OTX/pdb
EM Map EMD-70861: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Escherichia coli
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2025-05-27 Released: 2026-10-28
Deposition Author(s): Florez Ariza, A.J., Sosa, R., Bustamante, C.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 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

The central coupler of ClpXP controls intersubunit communication and couples intrasubunit chemical energy with force generation

Sosa, R.P., Florez Ariza, A.J., Kim, J., Tong, A.B., Kang, Z.H., Li, A., Kuriyan, J., Bustamante, C.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-78225-1

Macromolecule Content

Total Structure Weight: 607.2 kDa
Atom Count: 37,043
Modeled Residue Count: 4,759
Deposited Residue Count: 5,451
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpX	A, C, E	424	Escherichia coli	Mutation(s): 0 Gene Names: clpX, EcE24377A_0474
UniProt
Find proteins for A7ZIJ6 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZIJ6 Go to UniProtKB: A7ZIJ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7ZIJ6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpX	B, D, F	424	Escherichia coli	Mutation(s): 1 Gene Names: clpX, EcE24377A_0474
UniProt
Find proteins for A7ZIJ6 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZIJ6 Go to UniProtKB: A7ZIJ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7ZIJ6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	G, H, I, J, K G, H, I, J, K, L, M, N, O, P, Q, R, S, T	207	Escherichia coli	Mutation(s): 0 Gene Names: clpP, clpP_1, clpP_2, clpP_3, clpP_4 EC: 3.4.21.92
UniProt
Find proteins for C3TLT2 (Escherichia coli) Explore C3TLT2 Go to UniProtKB: C3TLT2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3TLT2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate	U	9	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
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain W [auth B] SDF format, chain DA [auth F] SDF format, chain CA [auth E] SDF format, chain AA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain W [auth B] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain W [auth B] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth D]	AA [auth D], CA [auth E], DA [auth F], 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 DA [auth F] Focus chain W [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain W [auth B] Focus chain Y [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain X [auth B] SDF format, chain BA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth B] MOL2 format, chain BA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain X [auth B] mmCIF format, chain BA [auth D]	BA [auth D], X [auth B], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain X [auth B] Focus chain Z [auth C]

Non-standard Monomers 1 Unique
ID	Chains	Type	Formula	2D Diagram
UNK Query on UNK	U	L-PEPTIDE LINKING	C₄ H₉ N O₂

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Florez Ariza, A.J.

Sosa, R.

Bustamante, C.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	R01GM032543