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- EMDB-58651: Human wild-type LONP1 bound to PZL-26 -

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Basic information

Entry
Database: EMDB / ID: EMD-58651
TitleHuman wild-type LONP1 bound to PZL-26
Map data
Sample
  • Organelle or cellular component: Recombinant human LONP1 expressed in bacterial cells, E. coli (Rosetta pLyss).
    • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: [(1~{R})-1-[[(2~{R})-4-morpholin-4-yl-4-oxidanylidene-2-(pyrazin-2-ylcarbonylamino)butanoyl]amino]-4-phenyl-butyl]boronic acid
KeywordsInhibitor / AAA+ protease / HYDROLASE
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 / mitochondrial nucleoid ...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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPardo-Hernandez C / Green J / Gustafsson CM
Funding support Sweden, 3 items
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 AM / Charifson PS / Phan C / Shi Y / Kern G / Martinez Botella G / Keating TA / Macao B / Larsson NG / ...Authors: Szilagyi Z / Michon P / Pardo-Hernandez C / Sacultanu M / Miralles Fuste J / Griffin AM / Charifson PS / Phan C / Shi Y / Kern G / Martinez Botella G / Keating TA / Macao B / Larsson NG / Falkenberg M / Green J / Gustafsson CM
History
DepositionJun 23, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58651.png

Downloads & links

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Map

FileDownload / File: emd_58651.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.051457986 - 0.07870276
Average (Standard dev.)0.00020335327 (±0.0019404624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58651_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58651_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_58651_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Recombinant human LONP1 expressed in bacterial cells, E. coli (Ro...

EntireName: Recombinant human LONP1 expressed in bacterial cells, E. coli (Rosetta pLyss).
Components
  • Organelle or cellular component: Recombinant human LONP1 expressed in bacterial cells, E. coli (Rosetta pLyss).
    • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: [(1~{R})-1-[[(2~{R})-4-morpholin-4-yl-4-oxidanylidene-2-(pyrazin-2-ylcarbonylamino)butanoyl]amino]-4-phenyl-butyl]boronic acid

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Supramolecule #1: Recombinant human LONP1 expressed in bacterial cells, E. coli (Ro...

SupramoleculeName: Recombinant human LONP1 expressed in bacterial cells, E. coli (Rosetta pLyss).
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Lon protease homolog, mitochondrial

MacromoleculeName: Lon protease homolog, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: endopeptidase La
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.553086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GFWEASSRGG GAFSGGEDAS EGGAEEGAGG AGGSAGAGEG PVITALTPMT IPDVFPHLPL IAITRNPVFP RFIKIIEVKN KKLVELLRR KVRLAQPYVG VFLKRDDSNE SDVVESLDEI YHTGTFAQIH EMQDLGDKLR MIVMGHRRVH ISRQLEVEPE E PEAENKHK ...String:
GFWEASSRGG GAFSGGEDAS EGGAEEGAGG AGGSAGAGEG PVITALTPMT IPDVFPHLPL IAITRNPVFP RFIKIIEVKN KKLVELLRR KVRLAQPYVG VFLKRDDSNE SDVVESLDEI YHTGTFAQIH EMQDLGDKLR MIVMGHRRVH ISRQLEVEPE E PEAENKHK PRRKSKRGKK EAEDELSARH PAELAMEPTP ELPAEVLMVE VENVVHEDFQ VTEEVKALTA EIVKTIRDII AL NPLYRES VLQMMQAGQR VVDNPIYLSD MGAALTGAES HELQDVLEET NIPKRLYKAL SLLKKEFELS KLQQRLGREV EEK IKQTHR KYLLQEQLKI IKKELGLEKD DKDAIEEKFR ERLKELVVPK HVMDVVDEEL SKLGLLDNHS SEFNVTRNYL DWLT SIPWG KYSNENLDLA RAQAVLEEDH YGMEDVKKRI LEFIAVSQLR GSTQGKILCF YGPPGVGKTS IARSIARALN REYFR FSVG GMTDVAEIKG HRRTYVGAMP GKIIQCLKKT KTENPLILID EVDKIGRGYQ GDPSSALLEL LDPEQNANFL DHYLDV PVD LSKVLFICTA NVTDTIPEPL RDRMEMINVS GYVAQEKLAI AERYLVPQAR ALCGLDESKA KLSSDVLTLL IKQYCRE SG VRNLQKQVEK VLRKSAYKIV SGEAESVEVT PENLQDFVGK PVFTVERMYD VTPPGVVMGL AWTAMGGSTL FVETSLRR P QDKDAKGDKD GSLEVTGQLG EVMKESARIA YTFARAFLMQ HAPANDYLVT SHIHLHVPEG ATPKDGPSAG CTIVTALLS LAMGRPVRQN LAMTGEVSLT GKILPVGGIK EKTIAAKRAG VTCIVLPAEN KKDFYDLAAF ITEGLEVHFV EHYREIFDIA FPDEQAEAL AVER

UniProtKB: Lon protease homolog, mitochondrial

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Macromolecule #2: [(1~{R})-1-[[(2~{R})-4-morpholin-4-yl-4-oxidanylidene-2-(pyrazin-...

MacromoleculeName: [(1~{R})-1-[[(2~{R})-4-morpholin-4-yl-4-oxidanylidene-2-(pyrazin-2-ylcarbonylamino)butanoyl]amino]-4-phenyl-butyl]boronic acid
type: ligand / ID: 2 / Number of copies: 6 / Formula: A1KDX
Molecular weightTheoretical: 483.325 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7p09

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.9) / Number images used: 209371
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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