31EP | pdb_000031ep

P1a-state of wild type human mitochondrial LONP1 protease with bound substrate protein, ADP and aluminum fluoride

PDB DOI: https://doi.org/10.2210/pdb31EP/pdb
EM Map EMD-58342: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Homo sapiens, Escherichia coli K-12
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2026-05-29 Released: 2026-06-17
Deposition Author(s): Schenck, N., Filipcik, P., Abrahams, J.P.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.54 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 31EP

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

Literature

Human mitochondrial Lon protease initiates unidirectional degradation from either substrate terminus

Schenck, N., Filipcik, P., Abrahams, J.P.

(null) bioRxiv

DOI: https://doi.org/10.64898/2026.05.18.725877

Macromolecule Content

Total Structure Weight: 583.76 kDa
Atom Count: 25,422
Modeled Residue Count: 3,248
Deposited Residue Count: 5,150
Unique protein chains: 2

Macromolecules

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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	854	Homo sapiens	Mutation(s): 0 EC: 3.4.21.53 (PDB Primary Data), 3.6.4.10 (UniProt)
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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown translocated polypeptide substrate	G, H	13	Escherichia coli K-12	Mutation(s): 0

Small Molecules

Ligands 3 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 L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain I [auth A]	I [auth A] L [auth B] O [auth C] R [auth D] U [auth E] I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], V [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth F]
AF3 (Subject of Investigation/LOI) Query on AF3 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain N [auth B]	K [auth A], N [auth B], Q [auth C], T [auth D]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	J [auth A], M [auth B], P [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.54 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2026-06-17
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.