Human mitochondrial LONP1 in complex with Bortezomib

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Structures of the human LONP1 protease reveal regulatory steps involved in protease activation.

Shin, M.Watson, E.R.Song, A.S.Mindrebo, J.T.Novick, S.J.Griffin, P.R.Wiseman, R.L.Lander, G.C.

(2021) Nat Commun 12: 3239-3239

  • DOI: https://doi.org/10.1038/s41467-021-23495-0
  • Primary Citation of Related Structures:  
    7KRZ, 7KSL, 7KSM

  • PubMed Abstract: 

    The human mitochondrial AAA+ protein LONP1 is a critical quality control protease involved in regulating diverse aspects of mitochondrial biology including proteostasis, electron transport chain activity, and mitochondrial transcription. As such, genetic or aging-associated imbalances in LONP1 activity are implicated in pathologic mitochondrial dysfunction associated with numerous human diseases. Despite this importance, the molecular basis for LONP1-dependent proteolytic activity remains poorly defined. Here, we solved cryo-electron microscopy structures of human LONP1 to reveal the underlying molecular mechanisms governing substrate proteolysis. We show that, like bacterial Lon, human LONP1 adopts both an open and closed spiral staircase orientation dictated by the presence of substrate and nucleotide. Unlike bacterial Lon, human LONP1 contains a second spiral staircase within its ATPase domain that engages substrate as it is translocated toward the proteolytic chamber. Intriguingly, and in contrast to its bacterial ortholog, substrate binding within the central ATPase channel of LONP1 alone is insufficient to induce the activated conformation of the protease domains. To successfully induce the active protease conformation in substrate-bound LONP1, substrate binding within the protease active site is necessary, which we demonstrate by adding bortezomib, a peptidomimetic active site inhibitor of LONP1. These results suggest LONP1 can decouple ATPase and protease activities depending on whether AAA+ or both AAA+ and protease domains bind substrate. Importantly, our structures provide a molecular framework to define the critical importance of LONP1 in regulating mitochondrial proteostasis in health and disease.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lon protease homolog, mitochondrial
A, B, C, D, E
A, B, C, D, E, F
534Homo sapiensMutation(s): 0 
Gene Names: LONP1PRSS15
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36776
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endogenous co-purified substrate12Escherichia coli BL21(DE3)Mutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
N [auth C],
Q [auth D]
C10 H16 N5 O13 P3
Query on ADP

Download Ideal Coordinates CCD File 
T [auth E],
V [auth F]
C10 H15 N5 O10 P2
Query on BO2

Download Ideal Coordinates CCD File 
J [auth A]
M [auth B]
P [auth C]
S [auth D]
U [auth E]
J [auth A],
M [auth B],
P [auth C],
S [auth D],
U [auth E],
W [auth F]
C19 H25 B N4 O4
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
O [auth C],
R [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG067594
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS095892
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG061697
National Institutes of Health/Office of the DirectorUnited StatesS10OD021634

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references