9CC3 | pdb_00009cc3

Human Mitochondrial LONP1 Stall State + casein

PDB DOI: https://doi.org/10.2210/pdb9CC3/pdb
EM Map EMD-45433: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Escherichia coli 'BL21-Gold(DE3)pLysS AG, Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-06-20 Released: 2024-08-07
Deposition Author(s): Mindrebo, J.T., Lander, G.C.
Funding Organization(s): 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: 3.23 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

Structural and mechanistic studies on human LONP1 redefine the hand-over-hand translocation mechanism.

Mindrebo, J.T., Lander, G.C.

(2024) bioRxiv

PubMed: 38979310 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/2024.06.24.600538
Primary Citation Related Structures:
9CC0, 9CC3

PubMed Abstract:
AAA+ enzymes use energy from ATP hydrolysis to remodel diverse cellular targets. Structures of substrate-bound AAA+ complexes suggest that these enzymes employ a conserved hand-over-hand mechanism to thread substrates through their central pore. However, the fundamental aspects of the mechanisms governing motor function and substrate processing within specific AAA+ families remain unresolved. We used cryo-electron microscopy to structurally interrogate reaction intermediates from in vitro biochemical assays to inform the underlying regulatory mechanisms of the human mitochondrial AAA+ protease, LONP1. Our results demonstrate that substrate binding allosterically regulates proteolytic activity, and that LONP1 can adopt a configuration conducive to substrate translocation even when the ATPases are bound to ADP. These results challenge the conventional understanding of the hand-over-hand translocation mechanism, giving rise to an alternative model that aligns more closely with biochemical and biophysical data on related enzymes like ClpX, ClpA, the 26S proteasome, and Lon protease.

Organizational Affiliation

Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA.

Macromolecule Content

Total Structure Weight: 589.19 kDa
Atom Count: 25,779
Modeled Residue Count: 3,353
Deposited Residue Count: 5,202
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endogenous Co-purified substrate modeled as unknown residues	A [auth G]	30	Escherichia coli 'BL21-Gold(DE3)pLysS AG	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lon protease homolog, mitochondrial	B [auth A] C [auth B] D [auth C] E [auth D] F [auth E] B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	862	Homo sapiens	Mutation(s): 0 Gene Names: LONP1, PRSS15 EC: 3.4.21.53
UniProt & NIH Common Fund Data Resources
Find proteins for P36776 (Homo sapiens) Explore P36776 Go to UniProtKB: P36776
PHAROS: P36776 GTEx: ENSG00000196365
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36776
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain N [auth E] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E]	H [auth B], J [auth C], L [auth D], N [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain I [auth B]	I [auth B], K [auth C], M [auth D], O [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Mindrebo, J.T.

Lander, G.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM145143
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS095892