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- PDB-31sy: Human wild-type LONP1 bound to PZL-26 -

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Basic information

Entry
Database: PDB / ID: 31sy
TitleHuman wild-type LONP1 bound to PZL-26
ComponentsLon protease homolog, mitochondrial
KeywordsHYDROLASE / Inhibitor / AAA+ protease
Function / homology
Function and homology information


oxidation-dependent protein catabolic process / response to aluminum ion / PH domain binding / endopeptidase La / mitochondrial protein catabolic process / G-quadruplex DNA binding / : / ATP-dependent peptidase activity / non-chaperonin molecular chaperone ATPase / protein quality control for misfolded or incompletely synthesized proteins ...oxidation-dependent protein catabolic process / response to aluminum ion / PH domain binding / endopeptidase La / mitochondrial protein catabolic process / G-quadruplex DNA binding / : / ATP-dependent peptidase activity / non-chaperonin molecular chaperone ATPase / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid / insulin receptor substrate binding / Mitochondrial unfolded protein response (UPRmt) / chaperone-mediated protein complex assembly / DNA polymerase binding / response to hormone / Mitochondrial protein degradation / mitochondrion organization / ADP binding / single-stranded DNA binding / cellular response to oxidative stress / sequence-specific DNA binding / response to hypoxia / single-stranded RNA binding / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / identical protein binding
Similarity search - Function
Lon protease homologue, chloroplastic/mitochondrial / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain ...Lon protease homologue, chloroplastic/mitochondrial / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Lon protease homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsPardo-Hernandez, C. / Green, J. / Gustafsson, C.M.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2021-00932 Sweden
Swedish Research Council2022-00976 Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: A selective inhibitor reveals roles for LONP1 in mitochondrial proteostasis and OXPHOS dependencies
Authors: Szilagyi, Z. / Michon, P. / Pardo-Hernandez, C. / Sacultanu, M. / Miralles Fuste, J. / Griffin, A.M. / Charifson, P.S. / Phan, C. / Shi, Y. / Kern, G. / Martinez Botella, G. / Keating, T.A. ...Authors: Szilagyi, Z. / Michon, P. / Pardo-Hernandez, C. / Sacultanu, M. / Miralles Fuste, J. / Griffin, A.M. / Charifson, P.S. / Phan, C. / Shi, Y. / Kern, G. / Martinez Botella, G. / Keating, T.A. / Macao, B. / Larsson, N.G. / Falkenberg, M. / Green, J. / Gustafsson, C.M.
History
DepositionJun 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lon protease homolog, mitochondrial
B: Lon protease homolog, mitochondrial
C: Lon protease homolog, mitochondrial
D: Lon protease homolog, mitochondrial
E: Lon protease homolog, mitochondrial
F: Lon protease homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)600,21812
Polymers597,3196
Non-polymers2,9006
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Lon protease homolog, mitochondrial / LONHs / Lon protease-like protein / LONP / Mitochondrial ATP-dependent protease Lon / Mitochondrial ...LONHs / Lon protease-like protein / LONP / Mitochondrial ATP-dependent protease Lon / Mitochondrial chaperone LONP1 / Serine protease 15


Mass: 99553.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LONP1, Lon, PRSS15 / Production host: Escherichia coli (E. coli)
References: UniProt: P36776, endopeptidase La, non-chaperonin molecular chaperone ATPase
#2: Chemical
ChemComp-A1KDX / [(1~{R})-1-[[(2~{R})-4-morpholin-4-yl-4-oxidanylidene-2-(pyrazin-2-ylcarbonylamino)butanoyl]amino]-4-phenyl-butyl]boronic acid


Mass: 483.325 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H30BN5O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Recombinant human LONP1 expressed in bacterial cells, E. coli (Rosetta pLyss).
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta pLyss
Buffer solutionpH: 8
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Scipion3.0.9particle selection
13RELION3.0.93D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209371 / Symmetry type: POINT
RefinementResolution: 3→118.29 Å / Cor.coef. Fo:Fc: 0.908 / SU B: 12.438 / SU ML: 0.222 / ESU R: 0.357
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.34325 --
obs0.34325 110555 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 91.905 Å2
Refinement stepCycle: 1 / Total: 8970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.0129168
ELECTRON MICROSCOPYr_bond_other_d00.0168766
ELECTRON MICROSCOPYr_angle_refined_deg1.571.85712438
ELECTRON MICROSCOPYr_angle_other_deg0.5351.76920226
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.32751140
ELECTRON MICROSCOPYr_dihedral_angle_2_deg5.075554
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.821101476
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0790.21422
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0210926
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021950
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it11.6848.1374596
ELECTRON MICROSCOPYr_mcbond_other11.6838.1374596
ELECTRON MICROSCOPYr_mcangle_it18.27614.565724
ELECTRON MICROSCOPYr_mcangle_other18.27514.5625725
ELECTRON MICROSCOPYr_scbond_it13.37710.1264572
ELECTRON MICROSCOPYr_scbond_other13.37810.1244571
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other22.28817.6966715
ELECTRON MICROSCOPYr_long_range_B_refined30.06699.1135583
ELECTRON MICROSCOPYr_long_range_B_other30.06699.1135584
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.089 8279 -
obs--100 %

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