22IB | pdb_000022ib

CryoEM structure of Human LonP1-TFAM complex

PDB DOI: https://doi.org/10.2210/pdb22IB/pdb
EM Map EMD-68281: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-01-12 Released: 2026-04-22
Deposition Author(s): Li, M., Liu, H., Zhang, K., Li, S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 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 Analysis of Human LonP1 Protease Bound with the Native Substrate.

Li, M., Liu, H., Zhang, S., Gao, Q., Li, S., Wang, J., Zhang, K.

(2026) Life (Basel) 16

PubMed: 41900996 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/life16030478
Primary Citation Related Structures:
22IB

PubMed Abstract:
The human mitochondrial Lon protease (LonP1) is a central regulator of mitochondrial DNA copy number and metabolic reprogramming. However, the structural basis for how LonP1 recognizes native physiological substrates remains elusive. Here, we present the high-resolution cryo-EM structure of the human LonP1 hexamer actively engaging its native substrate, TFAM. The reconstruction reveals a distinct bipartite search-and-shred mechanism. Unlike its bacterial homologs, the human N-terminal domain (NTD) adopts a compact architecture acting as a selective vestibule to recruit and initially unfold the substrate tertiary structure. Subsequently, the polypeptide is threaded through the central channel via a hand-over-hand mechanism driven by a spiral array of aromatic pore-loops. This structural framework provides a mechanistic rationale for the spatial segregation of LonP1 and offers a template for targeting mitochondrial proteostasis in human diseases.

Organizational Affiliation

Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.

Macromolecule Content

Total Structure Weight: 397.96 kDa
Atom Count: 26,569
Modeled Residue Count: 3,399
Deposited Residue Count: 3,538
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lon protease homolog, mitochondrial	A, B, C, D, E A, B, C, D, E, F	585	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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TFAM substrate	G	28	Homo sapiens	Mutation(s): 0

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 J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A], I [auth B], J [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain K [auth D] MOL2 format, chain M [auth E] MOL2 format, chain K [auth D] mmCIF format, chain M [auth E] mmCIF format, chain K [auth D]	K [auth D], M [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth D] Focus chain M [auth E] Interactions & Density Focus chain K [auth D] Focus chain M [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D]	L [auth D], N [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain L [auth D] Focus chain N [auth E]