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- EMDB-13147: Human mitochondrial Lon protease without substrate -

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Basic information

Entry
Database: EMDB / ID: EMD-13147
TitleHuman mitochondrial Lon protease without substrate
Map dataHuman mitochondrial LonP1 apo form
Sample
  • Complex: Human mitochondrial LonP1 G106P, R563W and K594M mutant
    • 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: 4.11 Å
AuthorsValentin Gese G / Shahzad S / Hallberg BM
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-
UpdateAug 11, 2021-
Current statusAug 11, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p0b
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13147.png

Downloads & links

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Map

FileDownload / File: emd_13147.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman mitochondrial LonP1 apo form
Voxel sizeX=Y=Z: 1.308 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.45640746 - 1.1447377
Average (Standard dev.)-0.00032273965 (±0.026768459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 523.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3081.3081.308
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z523.200523.200523.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.4561.145-0.000

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Supplemental data

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Half map: Human mitochondrial LonP1 apo form, half map A

Fileemd_13147_half_map_1.map
AnnotationHuman mitochondrial LonP1 apo form, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human mitochondrial LonP1 apo form, half map B

Fileemd_13147_half_map_2.map
AnnotationHuman mitochondrial LonP1 apo form, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human mitochondrial LonP1 G106P, R563W and K594M mutant

EntireName: Human mitochondrial LonP1 G106P, R563W and K594M mutant
Components
  • Complex: Human mitochondrial LonP1 G106P, R563W and K594M mutant
    • Protein or peptide: Lon protease homolog, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Human mitochondrial LonP1 G106P, R563W and K594M mutant

SupramoleculeName: Human mitochondrial LonP1 G106P, R563W and K594M mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: 98.664133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMGFWEASSR GGGAFSGGED ASEGGAEEGA GGAGGSAGAG EGGVITALTP MTIPDVFPHL PLIAITRNPV FPRFIKIIEV KNKKLVELL RRKVRLAQPY VGVFLKRDDS NESDVVESLD EIYHTGTFAQ IHEMQDLGDK LRMIVMGHRR VHISRQLEVE P EEPEAENK ...String:
SMGFWEASSR GGGAFSGGED ASEGGAEEGA GGAGGSAGAG EGGVITALTP 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 KGHRWTYVGA MPGKIIQCLK KTKTENPLIL IDEVDMIGRG 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

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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

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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61980
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3m6a


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7p0b:
Human mitochondrial Lon protease without substrate

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