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- EMDB-12307: P1b-state of wild type human mitochondrial LONP1 protease with bo... -

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Basic information

Entry
Database: EMDB / ID: EMD-12307
TitleP1b-state of wild type human mitochondrial LONP1 protease with bound endogenous substrate protein and in presence of ATP/ADP mix
Map data
Sample
  • Complex: P1b-state of hexameric LONP1 complex with ATP/ADP and bound endogenous substrate protein
    • Protein or peptide: Lon protease homolog, mitochondrial
    • Protein or peptide: substrate protein, chain G
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordshuman mitochondrial AAA+ protease / MOTOR PROTEIN
Function / homology
Function and homology information


oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / G-quadruplex DNA binding / endopeptidase La / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid ...oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / G-quadruplex DNA binding / endopeptidase La / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid / insulin receptor substrate binding / chaperone-mediated protein complex assembly / DNA polymerase binding / regulation of peptidyl-tyrosine phosphorylation / negative regulation of insulin receptor signaling pathway / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / mitochondrion organization / ADP binding / protein catabolic process / single-stranded DNA binding / cellular response to oxidative stress / sequence-specific DNA binding / single-stranded RNA binding / response to hypoxia / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / membrane / 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 N-terminal domain profile. ...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: 4.4 Å
AuthorsMohammed I / Schmitz KA
CitationJournal: Structure / Year: 2022
Title: Catalytic cycling of human mitochondrial Lon protease.
Authors: Inayathulla Mohammed / Kai A Schmitz / Niko Schenck / Dimitrios Balasopoulos / Annika Topitsch / Timm Maier / Jan Pieter Abrahams /
Abstract: The mitochondrial Lon protease (LonP1) regulates mitochondrial health by removing redundant proteins from the mitochondrial matrix. We determined LonP1 in eight nucleotide-dependent conformational ...The mitochondrial Lon protease (LonP1) regulates mitochondrial health by removing redundant proteins from the mitochondrial matrix. We determined LonP1 in eight nucleotide-dependent conformational states by cryoelectron microscopy (cryo-EM). The flexible assembly of N-terminal domains had 3-fold symmetry, and its orientation depended on the conformational state. We show that a conserved structural motif around T803 with a high similarity to the trypsin catalytic triad is essential for proteolysis. We show that LonP1 is not regulated by redox potential, despite the presence of two conserved cysteines at disulfide-bonding distance in its unfoldase core. Our data indicate how sequential ATP hydrolysis controls substrate protein translocation in a 6-fold binding change mechanism. Substrate protein translocation, rather than ATP hydrolysis, is a rate-limiting step, suggesting that LonP1 is a Brownian ratchet with ATP hydrolysis preventing translocation reversal. 3-fold rocking motions of the flexible N-domain assembly may assist thermal unfolding of the substrate protein.
History
DepositionFeb 8, 2021-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.262
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.262
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ng4
  • Surface level: 0.262
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12307.png

Downloads & links

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Map

FileDownload / File: emd_12307.map.gz / Format: CCP4 / Size: 343 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 448 pix.
= 372.288 Å		0.83 Å/pix.
x 448 pix.
= 372.288 Å		0.83 Å/pix.
x 448 pix.
= 372.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19 / Movie #1: 0.262
Minimum - Maximum-0.17364962 - 1.118098
Average (Standard dev.)0.004143334 (±0.051189903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 372.288 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8310.8310.831
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z372.288372.288372.288
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.1741.1180.004

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Supplemental data

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Mask #1

Fileemd_12307_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12307_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12307_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : P1b-state of hexameric LONP1 complex with ATP/ADP and bound endog...

EntireName: P1b-state of hexameric LONP1 complex with ATP/ADP and bound endogenous substrate protein
Components
  • Complex: P1b-state of hexameric LONP1 complex with ATP/ADP and bound endogenous substrate protein
    • Protein or peptide: Lon protease homolog, mitochondrial
    • Protein or peptide: substrate protein, chain G
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: P1b-state of hexameric LONP1 complex with ATP/ADP and bound endog...

SupramoleculeName: P1b-state of hexameric LONP1 complex with ATP/ADP and bound endogenous substrate protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 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: 96.288758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHGSMT IPDVFPHLPL IAITRNPVFP RFIKIIEVKN KKLVELLRRK VRLAQPYVGV FLKRDDSNES DVVESLDEIY HTGTFAQIH EMQDLGDKLR MIVMGHRRVH ISRQLEVEPE EPEAENKHKP RRKSKRGKKE AEDELSARHP AELAMEPTPE L PAEVLMVE ...String:
HHHHHHGSMT IPDVFPHLPL IAITRNPVFP RFIKIIEVKN KKLVELLRRK VRLAQPYVGV FLKRDDSNES DVVESLDEIY HTGTFAQIH EMQDLGDKLR MIVMGHRRVH ISRQLEVEPE EPEAENKHKP RRKSKRGKKE AEDELSARHP AELAMEPTPE L PAEVLMVE VENVVHEDFQ VTEEVKALTA EIVKTIRDII ALNPLYRESV LQMMQAGQRV VDNPIYLSDM GAALTGAESH EL QDVLEET NIPKRLYKAL SLLKKEFELS KLQQRLGREV EEKIKQTHRK YLLQEQLKII KKELGLEKDD KDAIEEKFRE RLK ELVVPK HVMDVVDEEL SKLGLLDNHS SEFNVTRNYL DWLTSIPWGK YSNENLDLAR AQAVLEEDHY GMEDVKKRIL EFIA VSQLR GSTQGKILCF YGPPGVGKTS IARSIARALN REYFRFSVGG MTDVAEIKGH RRTYVGAMPG KIIQCLKKTK TENPL ILID EVDKIGRGYQ GDPSSALLEL LDPEQNANFL DHYLDVPVDL SKVLFICTAN VTDTIPEPLR DRMEMINVSG YVAQEK LAI AERYLVPQAR ALCGLDESKA KLSSDVLTLL IKQYCRESGV RNLQKQVEKV LRKSAYKIVS GEAESVEVTP ENLQDFV GK PVFTVERMYD VTPPGVVMGL AWTAMGGSTL FVETSLRRPQ DKDAKGDKDG SLEVTGQLGE VMKESARIAY TFARAFLM Q HAPANDYLVT SHIHLHVPEG ATPKDGPSAG CTIVTALLSL AMGRPVRQNL AMTGEVSLTG KILPVGGIKE KTIAAKRAG VTCIVLPAEN KKDFYDLAAF ITEGLEVHFV EHYREIFDIA FPDEQAEALA VER

UniProtKB: Lon protease homolog, mitochondrial

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Macromolecule #2: substrate protein, chain G

MacromoleculeName: substrate protein, chain G / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.698783 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, 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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / 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

Concentration0.45 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 31607
Startup modelType of model: NONE / Details: ab-initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 31607
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7ng4:
P1b-state of wild type human mitochondrial LONP1 protease with bound endogenous substrate protein and in presence of ATP/ADP mix

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