9Y5M | pdb_00009y5m

LONP1 C3-state

PDB DOI: https://doi.org/10.2210/pdb9Y5M/pdb
EM Map EMD-72513: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-04 Released: 2026-08-12
Deposition Author(s): Mindrebo, J.T., Lander, G.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Y5M

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

Literature

Cryo-EM Reveals Regulatory Mechanisms Governing Substrate Selection and Activation of Human LONP1

Mindrebo, J.T., Alexandrescu, L., Baker, J.R., Wang, G., Lander, G.C.

(2025) Elife

DOI: https://doi.org/10.7554/elife.109186.1

Macromolecule Content

Total Structure Weight: 587.37 kDa
Atom Count: 26,393
Modeled Residue Count: 3,365
Deposited Residue Count: 5,172
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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	862	Homo sapiens	Mutation(s): 0 Gene Names: LONP1, PRSS15 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
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 1 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 F] SDF format, chain K [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NS095892

Revision History (Full details and data files)

Version 1.0: 2026-08-12
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.