[English] 日本語
Yorodumi
- EMDB-72514: LONP1 C2-state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72514
TitleLONP1 C2-state
Map dataLONP1-C2 sharpened consensus map
Sample
  • Organelle or cellular component: LONP1 in a C2-symmetric conformation
    • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
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: 3.35 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

-
Structure visualization

Supplemental images

emd_72514.png

Downloads & links

-
Map

FileDownload / File: emd_72514.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLONP1-C2 sharpened consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. 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: 0.25
Minimum - Maximum-0.7234218 - 1.4307047
Average (Standard dev.)0.00028476215 (±0.038798857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: LONP1-C2 unsharpened consensus map

Fileemd_72514_additional_1.map
AnnotationLONP1-C2 unsharpened consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: LONP1-C2 consensus half map A

Fileemd_72514_half_map_1.map
AnnotationLONP1-C2 consensus half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: LONP1-C2 consensus half map B

Fileemd_72514_half_map_2.map
AnnotationLONP1-C2 consensus half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LONP1 in a C2-symmetric conformation

EntireName: LONP1 in a C2-symmetric conformation
Components
  • Organelle or cellular component: LONP1 in a C2-symmetric conformation
    • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: LONP1 in a C2-symmetric conformation

SupramoleculeName: LONP1 in a C2-symmetric conformation / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Organelle: mitochondria / Location in cell: matrix
Molecular weightTheoretical: 584 KDa

-
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: 97.468156 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHENL YFQGAHMMTI PDVFPHLPLI AITRNPVFPR FIKIIEVKNK KLVELLRRKV RLAQPYVGVF LKRDDSNESD VVESLDEIY HTGTFAQIHE MQDLGDKLRM IVMGHRRVHI SRQLEVEPEE PEAENKHKPR RKSKRGKKEA EDELSARHPA E LAMEPTPE ...String:
MHHHHHHENL YFQGAHMMTI PDVFPHLPLI AITRNPVFPR FIKIIEVKNK KLVELLRRKV RLAQPYVGVF LKRDDSNESD VVESLDEIY HTGTFAQIHE MQDLGDKLRM IVMGHRRVHI SRQLEVEPEE PEAENKHKPR RKSKRGKKEA EDELSARHPA E LAMEPTPE LPAEVLMVEV ENVVHEDFQV TEEVKALTAE IVKTIRDIIA LNPLYRESVL QMMQAGQRVV DNPIYLSDMG AA LTGAESH ELQDVLEETN IPKRLYKALS LLKKEFELSK LQQRLGREVE EKIKQTHRKY LLQEQLKIIK KELGLEKDDK DAI EEKFRE RLKELVVPKH VMDVVDEELS KLGLLDNHSS EFNVTRNYLD WLTSIPWGKY SNENLDLARA QAVLEEDHYG MEDV KKRIL EFIAVSQLRG STQGKILCFY GPPGVGKTSI ARSIARALNR EYFRFSVGGM TDVAEIKGHR RTYVGAMPGK IIQCL KKTK TENPLILIDE VDKIGRGYQG DPSSALLELL DPEQNANFLD HYLDVPVDLS KVLFICTANV TDTIPEPLRD RMEMIN VSG YVAQEKLAIA ERYLVPQARA LCGLDESKAK LSSDVLTLLI KQYCRESGVR NLQKQVEKVL RKSAYKIVSG EAESVEV TP ENLQDFVGKP VFTVERMYDV TPPGVVMGLA WTAMGGSTLF VETSLRRPQD KDAKGDKDGS LEVTGQLGEV MKESARIA Y TFARAFLMQH APANDYLVTS HIHLHVPEGA TPKDGPSAGC TIVTALLSLA MGRPVRQNLA MTGEVSLTGK ILPVGGIKE KTIAAKRAGV TCIVLPAENK KDFYDLAAFI TEGLEVHFVE HYREIFDIAF PDEQAEALAV ER

UniProtKB: Lon protease homolog, mitochondrial

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was monodisperse and well behaved

-
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

+
Image processing

Particle selectionNumber selected: 1640000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42148
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7krz


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

PDB-9y5n:
LONP1 C2-state

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more