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- EMDB-72517: Open form of LONP1, LONP1-OFF -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72517
TitleOpen form of LONP1, LONP1-OFF
Map dataUnsharpened consensus map of open form of LONP1 (LONP1-OFF)
Sample
  • Organelle or cellular component: LONP1 Intermediate 3
    • Protein or peptide: LONP1
KeywordsAAA+ / Lon / LONP1 / protease / Regulatory state / TRANSLOCASE
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: 3.7 Å
AuthorsMindrebo JT / Lander GC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NS095892 United States
CitationJournal: Elife / Year: 2025
Title: Cryo-EM Reveals Regulatory Mechanisms Governing Substrate Selection and Activation of Human LONP1
Authors: Mindrebo JT / Alexandrescu L / Baker JR / Wang G / Lander GC
History
DepositionSep 4, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72517.png

Downloads & links

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Map

FileDownload / File: emd_72517.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened consensus map of open form of LONP1 (LONP1-OFF)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.23100221 - 0.67176545
Average (Standard dev.)0.00041017478 (±0.024490183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 331.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: LONP1-OFF Local refinement of NTD3H and CCD

Fileemd_72517_additional_1.map
AnnotationLONP1-OFF Local refinement of NTD3H and CCD
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: LONP1-OFF Half Map A

Fileemd_72517_half_map_1.map
AnnotationLONP1-OFF Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: LONP1-OFF Half Map A

Fileemd_72517_half_map_2.map
AnnotationLONP1-OFF Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LONP1 Intermediate 3

EntireName: LONP1 Intermediate 3
Components
  • Organelle or cellular component: LONP1 Intermediate 3
    • Protein or peptide: LONP1

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Supramolecule #1: LONP1 Intermediate 3

SupramoleculeName: LONP1 Intermediate 3 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organelle: mitochondria / Location in cell: matrix
Molecular weightTheoretical: 584 KDa

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Macromolecule #1: LONP1

MacromoleculeName: LONP1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: endopeptidase La
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQGAHMMTI PDVFPHLPLI AITRNPVFPR FIKIIEVKNK KLVELLRRKV RLAQPYVGVF LKRDDSNESD VVESLDEIYH TGTFAQIHEM QDLGDKLRMI VMGHRRVHIS RQLEVEPEEP EAENKHKPRR KSKRGKKEAE DELSARHPAE LAMEPTPELP ...String:
MHHHHHHENL YFQGAHMMTI PDVFPHLPLI AITRNPVFPR FIKIIEVKNK KLVELLRRKV RLAQPYVGVF LKRDDSNESD VVESLDEIYH TGTFAQIHEM QDLGDKLRMI VMGHRRVHIS RQLEVEPEEP EAENKHKPRR KSKRGKKEAE DELSARHPAE LAMEPTPELP AEVLMVEVEN VVHEDFQVTE EVKALTAEIV KTIRDIIALN PLYRESVLQM MQAGQRVVDN PIYLSDMGAA LTGAESHELQ DVLEETNIPK RLYKALSLLK KEFELSKLQQ RLGREVEEKI KQTHRKYLLQ EQLKIIKKEL GLEKDDKDAI EEKFRERLKE LVVPKHVMDV VDEELSKLGL LDNHSSEFNV TRNYLDWLTS IPWGKYSNEN LDLARAQAVL EEDHYGMEDV KKRILEFIAV SQLRGSTQGK ILCFYGPPGV GKTSIARSIA RALNREYFRF SVGGMTDVAE IKGHRRTYVG AMPGKIIQCL KKTKTENPLI LIDEVDKIGR GYQGDPSSAL LELLDPEQNA NFLDHYLDVP VDLSKVLFIC TANVTDTIPE PLRDRMEMIN VSGYVAQEKL AIAERYLVPQ ARALCGLDES KAKLSSDVLT LLIKQYCRES GVRNLQKQVE KVLRKSAYKI VSGEAESVEV TPENLQDFVG KPVFTVERMY DVTPPGVVMG LAWTAMGGST LFVETSLRRP QDKDAKGDKD GSLEVTGQLG EVMKESARIA YTFARAFLMQ HAPANDYLVT SHIHLHVPEG ATPKDGPSAG CTIVTALLSL AMGRPVRQNL AMTGEVSLTG KILPVGGIKE KTIAAKRAGV TCIVLPAENK KDFYDLAAFI TEGLEVHFVE HYREIFDIAF PDEQAEALAV ER

UniProtKB: Lon protease homolog, mitochondrial

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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

Concentration3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was monodisperse and well behaved

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 5775 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.81 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 73000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1640000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 42191
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7krz


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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