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- EMDB-13146: Human mitochondrial Lon protease with substrate in the ATPase domain -

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Basic information

Entry
Database: EMDB / ID: EMD-13146
TitleHuman mitochondrial Lon protease with substrate in the ATPase domain
Map dataComposite map of human mitochondrial LonP1
Sample
  • Complex: Composite map of human mitochondrial LonP1
    • Protein or peptide: Lon protease homolog, mitochondrial
    • Protein or peptide: Unknown peptide from human mitochondrial transcription factor A (TFAM)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsProtease / Mitochondria / AAA+ / HYDROLASE
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: 2.7 Å
AuthorsValentin Gese G / Shahzad S
CitationJournal: To Be Published
Title: A dual allosteric pathway drives human mitochondrial Lon
Authors: Valentin Gese G / Shahzad S / Pardo-Hernandez C / Wramstedt A / Falkenberg M / Hallberg M
History
DepositionJun 29, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7p09
  • Surface level: 4.3
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7p09
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13146.png

Downloads & links

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Map

FileDownload / File: emd_13146.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of human mitochondrial LonP1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 600 pix.
= 392.4 Å		0.65 Å/pix.
x 600 pix.
= 392.4 Å		0.65 Å/pix.
x 600 pix.
= 392.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.3 / Movie #1: 4.3
Minimum - Maximum-15.64781 - 46.896652000000003
Average (Standard dev.)0.04460557 (±0.6836022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 392.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6540.6540.654
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z392.400392.400392.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-15.64846.8970.045

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Supplemental data

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Additional map: Human mitochondrial LonP1 protease, ATPase domain focus

Fileemd_13146_additional_1.map
AnnotationHuman mitochondrial LonP1 protease, ATPase domain focus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human mitochondrial LonP1 protease, Lan domain focus

Fileemd_13146_additional_2.map
AnnotationHuman mitochondrial LonP1 protease, Lan domain focus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human mitochondrial LonP1 protease, protease domain focus

Fileemd_13146_additional_3.map
AnnotationHuman mitochondrial LonP1 protease, protease domain focus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Composite map of human mitochondrial LonP1

EntireName: Composite map of human mitochondrial LonP1
Components
  • Complex: Composite map of human mitochondrial LonP1
    • Protein or peptide: Lon protease homolog, mitochondrial
    • Protein or peptide: Unknown peptide from human mitochondrial transcription factor A (TFAM)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Composite map of human mitochondrial LonP1

SupramoleculeName: Composite map of human mitochondrial LonP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Composite map of three maps refined with a focus on the Lan domains, the ATPase domains and the protease domains, respectively
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 591 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: 98.673164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMGFWEASSR GGGAFSGGED ASEGGAEEGA GGAGGSAGAG EGPVITALTP MTIPDVFPHL PLIAITRNPV FPRFIKIIEV KNKKLVELL RRKVRLAQPY VGVFLKRDDS NESDVVESLD EIYHTGTFAQ IHEMQDLGDK LRMIVMGHRR VHISRQLEVE P EEPEAENK ...String:
SMGFWEASSR GGGAFSGGED ASEGGAEEGA GGAGGSAGAG EGPVITALTP MTIPDVFPHL PLIAITRNPV FPRFIKIIEV KNKKLVELL RRKVRLAQPY VGVFLKRDDS NESDVVESLD EIYHTGTFAQ IHEMQDLGDK LRMIVMGHRR VHISRQLEVE P EEPEAENK HKPRRKSKRG KKEAEDELSA RHPAELAMEP TPELPAEVLM VEVENVVHED FQVTEEVKAL TAEIVKTIRD II ALNPLYR ESVLQMMQAG QRVVDNPIYL SDMGAALTGA ESHELQDVLE ETNIPKRLYK ALSLLKKEFE LSKLQQRLGR EVE EKIKQT HRKYLLQEQL KIIKKELGLE KDDKDAIEEK FRERLKELVV PKHVMDVVDE ELSKLGLLDN HSSEFNVTRN YLDW LTSIP WGKYSNENLD LARAQAVLEE DHYGMEDVKK RILEFIAVSQ LRGSTQGKIL CFYGPPGVGK TSIARSIARA LNREY FRFS VGGMTDVAEI KGHRRTYVGA MPGKIIQCLK KTKTENPLIL IDEVDKIGRG YQGDPSSALL ELLDPEQNAN FLDHYL DVP VDLSKVLFIC TANVTDTIPE PLRDRMEMIN VSGYVAQEKL AIAERYLVPQ ARALCGLDES KAKLSSDVLT LLIKQYC RE SGVRNLQKQV EKVLRKSAYK IVSGEAESVE VTPENLQDFV GKPVFTVERM YDVTPPGVVM GLAWTAMGGS TLFVETSL R RPQDKDAKGD KDGSLEVTGQ LGEVMKESAR IAYTFARAFL MQHAPANDYL VTSHIHLHVP EGATPKDGPS AGCTIVTAL LSLAMGRPVR QNLAMTGEVS LTGKILPVGG IKEKTIAAKR AGVTCIVLPA ENKKDFYDLA AFITEGLEVH FVEHYREIFD IAFPD

UniProtKB: Lon protease homolog, mitochondrial

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Macromolecule #2: Unknown peptide from human mitochondrial transcription factor A (TFAM)

MacromoleculeName: Unknown peptide from human mitochondrial transcription factor A (TFAM)
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 954.168 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF
Details: This is a combined map from three focused refienements. The Lan domain, the ATPase domain and the protease domain focused maps with a 0.143 FSC resolution of 7.4, 2.7 and 2.75 angstroms.
Number images used: 152455
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

3m6a


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7p09:
Human mitochondrial Lon protease with substrate in the ATPase domain

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