P1a-state of wild type human mitochondrial LONP1 protease with bound substrate protein and ATPgS

Experimental Data Snapshot

  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 3.2 of the entry. See complete history


Catalytic cycling of human mitochondrial Lon protease.

Mohammed, I.Schmitz, K.A.Schenck, N.Balasopoulos, D.Topitsch, A.Maier, T.Abrahams, J.P.

(2022) Structure 30: 1254-1268.e7

  • DOI: https://doi.org/10.1016/j.str.2022.06.006
  • Primary Citation of Related Structures:  
    7NFY, 7NG4, 7NG5, 7NGC, 7NGF, 7NGL, 7NGP, 7NGQ, 7OXO

  • PubMed Abstract: 

    The mitochondrial Lon protease (LonP1) regulates mitochondrial health by removing redundant proteins from the mitochondrial matrix. We determined LonP1 in eight nucleotide-dependent conformational states by cryoelectron microscopy (cryo-EM). The flexible assembly of N-terminal domains had 3-fold symmetry, and its orientation depended on the conformational state. We show that a conserved structural motif around T803 with a high similarity to the trypsin catalytic triad is essential for proteolysis. We show that LonP1 is not regulated by redox potential, despite the presence of two conserved cysteines at disulfide-bonding distance in its unfoldase core. Our data indicate how sequential ATP hydrolysis controls substrate protein translocation in a 6-fold binding change mechanism. Substrate protein translocation, rather than ATP hydrolysis, is a rate-limiting step, suggesting that LonP1 is a Brownian ratchet with ATP hydrolysis preventing translocation reversal. 3-fold rocking motions of the flexible N-domain assembly may assist thermal unfolding of the substrate protein.

  • Organizational Affiliation

    Biozentrum, University of Basel, Basel, Switzerland.

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
853Homo 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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
substrate protein55Homo sapiensMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
L [auth C],
N [auth D],
Q [auth F]
C10 H16 N5 O12 P3 S
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
MG (Subject of Investigation/LOI)
Query on MG

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

Experimental Data

  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 2.0: 2021-08-25
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.0: 2022-08-10
    Changes: Atomic model, Database references
  • Version 3.1: 2022-09-14
    Changes: Database references
  • Version 3.2: 2022-11-09
    Changes: Database references