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- EMDB-58849: R0-state of wild type human mitochondrial LONP1 protease bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-58849
TitleR0-state of wild type human mitochondrial LONP1 protease bound to endogenous ADP
Map data
Sample
  • Complex: Lon protease homolog, mitochondrial
    • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA+ protease / Lon protease / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsSchenck N / Roesgaard MA / Abrahams JP
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Other government Switzerland
CitationJournal: To Be Published
Title: Mitochondrial Lon protease couples substrate translocation to proteolytic activation
Authors: Schenck N / Roesgaard MA / Abrahams JP
History
DepositionJul 8, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58849.png

Downloads & links

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Map

FileDownload / File: emd_58849.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 512 pix.
= 449.536 Å		0.88 Å/pix.
x 512 pix.
= 449.536 Å		0.88 Å/pix.
x 512 pix.
= 449.536 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.1258681 - 0.34333894
Average (Standard dev.)-0.00024347457 (±0.008727831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 449.536 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58849_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_58849_half_map_1.map
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Histogram

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Half map: #1

Fileemd_58849_half_map_2.map
Projections & Slices
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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: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Lon protease homolog, mitochondrial

SupramoleculeName: Lon protease homolog, mitochondrial / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: R0-state of wild type human mitochondrial LONP1 protease bound to endogenous ADP
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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / 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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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 (0.7 mg/mL) were incubated in buffer (50 mM HEPES, 150 mM NaCl, 5 mM MgCl2, pH 7.5) for 30 min at room temperature.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

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

7ngl

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 71544
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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