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- EMDB-13102: human LonP1, R-state, incubated in AMPPCP -

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Basic information

Entry
Database: EMDB / ID: EMD-13102
Titlehuman LonP1, R-state, incubated in AMPPCP
Map dataLonP1, R-state, ADP bound, incubated in AMPPCP
Sample
  • Complex: human mitochondrial Lon protease homolog
    • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


oxidation-dependent protein catabolic process / PH domain binding / endopeptidase La / G-quadruplex DNA binding / response to aluminum ion / 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 / endopeptidase La / G-quadruplex DNA binding / response to aluminum ion / 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 / mitochondrion organization / proteolysis involved in protein catabolic process / response to hormone / 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 / membrane / identical protein binding / cytosol
Similarity search - Function
Lon protease homologue, chloroplastic/mitochondrial / Lon protease, bacterial/eukaryotic-type / 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, N-terminal domain superfamily / Lon N-terminal domain profile. ...Lon protease homologue, chloroplastic/mitochondrial / Lon protease, bacterial/eukaryotic-type / 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, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / 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: 3.9 Å
AuthorsAbrahams JP / Mohammed I / Schmitz KA / Schenck N / Maier T
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_165669 Switzerland
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
DepositionJun 22, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oxo
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13102.png

Downloads & links

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Map

FileDownload / File: emd_13102.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLonP1, R-state, ADP bound, incubated in AMPPCP
Voxel sizeX=Y=Z: 1.058 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.15
Minimum - Maximum-1.1495754 - 2.4745212
Average (Standard dev.)-0.0038650015 (±0.05963097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z423.200423.200423.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.1502.475-0.004

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Supplemental data

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Sample components

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Entire : human mitochondrial Lon protease homolog

EntireName: human mitochondrial Lon protease homolog
Components
  • Complex: human mitochondrial Lon protease homolog
    • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: human mitochondrial Lon protease homolog

SupramoleculeName: human mitochondrial Lon protease homolog / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 639 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: 106.635375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAASTGYVRL WGAARCWVLR RPMLAAAGGR VPTAAGAWLL RGQRTCDASP PWALWGRGPA IGGQWRGFWE ASSRGGGAFS GGEDASEGG AEEGAGGAGG SAGAGEGPVI TALTPMTIPD VFPHLPLIAI TRNPVFPRFI KIIEVKNKKL VELLRRKVRL A QPYVGVFL ...String:
MAASTGYVRL WGAARCWVLR RPMLAAAGGR VPTAAGAWLL RGQRTCDASP PWALWGRGPA IGGQWRGFWE ASSRGGGAFS GGEDASEGG AEEGAGGAGG SAGAGEGPVI TALTPMTIPD VFPHLPLIAI TRNPVFPRFI KIIEVKNKKL VELLRRKVRL A QPYVGVFL KRDDSNESDV VESLDEIYHT GTFAQIHEMQ DLGDKLRMIV MGHRRVHISR QLEVEPEEPE AENKHKPRRK SK RGKKEAE DELSARHPAE LAMEPTPELP AEVLMVEVEN VVHEDFQVTE EVKALTAEIV KTIRDIIALN PLYRESVLQM MQA GQRVVD NPIYLSDMGA ALTGAESHEL QDVLEETNIP KRLYKALSLL KKEFELSKLQ QRLGREVEEK IKQTHRKYLL QEQL KIIKK ELGLEKDDKD AIEEKFRERL KELVVPKHVM DVVDEELSKL GLLDNHSSEF NVTRNYLDWL TSIPWGKYSN ENLDL ARAQ AVLEEDHYGM EDVKKRILEF IAVSQLRGST QGKILCFYGP PGVGKTSIAR SIARALNREY FRFSVGGMTD VAEIKG HRR TYVGAMPGKI IQCLKKTKTE NPLILIDEVD KIGRGYQGDP SSALLELLDP EQNANFLDHY LDVPVDLSKV LFICTAN VT DTIPEPLRDR MEMINVSGYV AQEKLAIAER YLVPQARALC GLDESKAKLS SDVLTLLIKQ YCRESGVRNL QKQVEKVL R KSAYKIVSGE AESVEVTPEN LQDFVGKPVF TVERMYDVTP PGVVMGLAWT AMGGSTLFVE TSLRRPQDKD AKGDKDGSL EVTGQLGEVM KESARIAYTF ARAFLMQHAP ANDYLVTSHI HLHVPEGATP KDGPSAGCTI VTALLSLAMG RPVRQNLAMT GEVSLTGKI LPVGGIKEKT IAAKRAGVTC IVLPAENKKD FYDLAAFITE GLEVHFVEHY REIFDIAFPD EQAEALAVER

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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 / Adenosine diphosphate

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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

Concentration0.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2
Details: Dat collected in movie mode, 79850 particles used for map reconstruction
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 236000 / Details: used 79850 particles for final reconstruction
CTF correctionSoftware - Name: RELION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ngl


Details: LonP1 R-state, incubated in the presence of ATP and ADP
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79850

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Atomic model buiding 1

Initial modelPDB ID:

7ngl

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 186 / Target criteria: Correlation coefficient
Output model

PDB-7oxo:
human LonP1, R-state, incubated in AMPPCP

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