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- EMDB-58342: P1a-state of wild type human mitochondrial LONP1 protease with bo... -

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Basic information

Entry
Database: EMDB / ID: EMD-58342
TitleP1a-state of wild type human mitochondrial LONP1 protease with bound substrate protein, ADP and aluminum fluoride
Map data
Sample
  • Complex: Lon protease homolog, mitochondrial
    • Protein or peptide: unknown translocated polypeptide substrate
  • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ALUMINUM FLUORIDE
KeywordsAAA+ protease / Lon protease / transition state / MOTOR PROTEIN
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 / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid / insulin receptor substrate binding ...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 / 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 / negative regulation of insulin receptor signaling pathway / 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 / nucleoplasm / ATP binding / membrane / identical protein binding / cytosol
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) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsSchenck N / Filipcik P / Abrahams JP
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Other government Switzerland
CitationJournal: biorxiv
Title: Human mitochondrial Lon protease initiates unidirectional degradation from either substrate terminus
Authors: Schenck N / Filipcik P / Abrahams JP
History
DepositionMay 29, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58342.png

Downloads & links

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Map

FileDownload / File: emd_58342.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.21093144 - 0.6633781
Average (Standard dev.)0.00002849797 (±0.011671226)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_58342_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_58342_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lon protease homolog, mitochondrial

EntireName: Lon protease homolog, mitochondrial
Components
  • Complex: Lon protease homolog, mitochondrial
    • Protein or peptide: unknown translocated polypeptide substrate
  • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ALUMINUM FLUORIDE

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Supramolecule #1: Lon protease homolog, mitochondrial

SupramoleculeName: Lon protease homolog, mitochondrial / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Details: P1a-state of wild type human mitochondrial LONP1 protease with bound substrate protein, ADP and aluminum fluoride
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 585 KDa

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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: 96.419953 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MHHHHHHGSM TIPDVFPHLP LIAITRNPVF PRFIKIIEVK NKKLVELLRR KVRLAQPYVG VFLKRDDSNE SDVVESLDEI YHTGTFAQI HEMQDLGDKL RMIVMGHRRV HISRQLEVEP EEPEAENKHK PRRKSKRGKK EAEDELSARH PAELAMEPTP E LPAEVLMV ...String:
MHHHHHHGSM TIPDVFPHLP LIAITRNPVF PRFIKIIEVK NKKLVELLRR KVRLAQPYVG VFLKRDDSNE SDVVESLDEI YHTGTFAQI HEMQDLGDKL RMIVMGHRRV HISRQLEVEP EEPEAENKHK PRRKSKRGKK EAEDELSARH PAELAMEPTP E LPAEVLMV EVENVVHEDF QVTEEVKALT AEIVKTIRDI IALNPLYRES VLQMMQAGQR VVDNPIYLSD MGAALTGAES HE LQDVLEE TNIPKRLYKA LSLLKKEFEL SKLQQRLGRE VEEKIKQTHR KYLLQEQLKI IKKELGLEKD DKDAIEEKFR ERL KELVVP KHVMDVVDEE LSKLGLLDNH SSEFNVTRNY LDWLTSIPWG KYSNENLDLA RAQAVLEEDH YGMEDVKKRI LEFI AVSQL RGSTQGKILC FYGPPGVGKT SIARSIARAL NREYFRFSVG GMTDVAEIKG HRRTYVGAMP GKIIQCLKKT KTENP LILI DEVDKIGRGY QGDPSSALLE LLDPEQNANF LDHYLDVPVD LSKVLFICTA NVTDTIPEPL RDRMEMINVS GYVAQE KLA IAERYLVPQA RALCGLDESK AKLSSDVLTL LIKQYCRESG VRNLQKQVEK VLRKSAYKIV SGEAESVEVT PENLQDF VG KPVFTVERMY DVTPPGVVMG LAWTAMGGST LFVETSLRRP QDKDAKGDKD GSLEVTGQLG EVMKESARIA YTFARAFL M QHAPANDYLV TSHIHLHVPE GATPKDGPSA GCTIVTALLS LAMGRPVRQN LAMTGEVSLT GKILPVGGIK EKTIAAKRA GVTCIVLPAE NKKDFYDLAA FITEGLEVHF VEHYREIFDI AFPDEQAEAL AVER

UniProtKB: Lon protease homolog, mitochondrial

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Macromolecule #2: unknown translocated polypeptide substrate

MacromoleculeName: unknown translocated polypeptide substrate / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 1.124378 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 5 / Number of copies: 4 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

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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

BufferpH: 7.5
Details: Pure LonP1 fractions (1.0 mg/mL) were incubated with 1 mM ADP in SEC buffer (50 mM HEPES, 150 mM NaCl, 5 mM MgCl2, pH 7.5) for 20 min at room temperature. Subsequently, 3.125 mM NaF was ...Details: Pure LonP1 fractions (1.0 mg/mL) were incubated with 1 mM ADP in SEC buffer (50 mM HEPES, 150 mM NaCl, 5 mM MgCl2, pH 7.5) for 20 min at room temperature. Subsequently, 3.125 mM NaF was added, followed by 0.625 mM AlCl3 after additional 20 min incubation for each step to generate the LonP1-ADP-AlF3 complex.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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:

7nfy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 180065
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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