9CC1 | pdb_00009cc1

Human Mitochondrial LONP1 Idle State bound to substrate and 6 ADP

PDB DOI: https://doi.org/10.2210/pdb9CC1/pdb
EM Map EMD-45431: EMDB EMDataResource

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

Deposited: 2024-06-20 Released: 2025-04-30
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: 2.92 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.

To be published.

Macromolecule Content

Total Structure Weight: 588.56 kDa
Atom Count: 24,523
Modeled Residue Count: 3,135
Deposited Residue Count: 5,184
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bound substrate segment undergoing degradation	A [auth G]	12	Bos taurus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 R [auth F] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] M [auth C] O [auth D] P [auth E] I [auth A], K [auth B], M [auth C], O [auth D], P [auth E], R [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] Q [auth E] H [auth A], J [auth B], L [auth C], N [auth D], Q [auth E], S [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [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
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

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