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- PDB-8ojl: Human Mitochondrial Lon Y394E Mutant ADP Bound -

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Basic information

Entry
Database: PDB / ID: 8ojl
TitleHuman Mitochondrial Lon Y394E Mutant ADP Bound
ComponentsLon protease homolog, mitochondrial
KeywordsHYDROLASE / Human mitochondrial AAA+ protease / motor protein
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
ADENOSINE-5'-DIPHOSPHATE / Lon protease homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsKereiche, S. / Bauer, J.A. / Matyas, P. / Novacek, J. / Kutejova, E.
Funding supportEuropean Union, Czech Republic, 7items
OrganizationGrant numberCountry
Other governmentAPVV-15-0375
Other governmentAPVV-19-0298
Other governmentVEGA-2/0069/23
Other governmentVEGA-2/0131/20
European Regional Development FundITMS:305011X666European Union
Ministry of Education, Youth and Sports of the Czech RepublicCIISB project LM2018127 Czech Republic
Czech Science Foundation1825144Y Czech Republic
CitationJournal: To Be Published
Title: Phosphorylation of the N-terminal domain of human mitochondrial Lon protease disrupts its functions.
Authors: Ondrovicova, G. / Kunova, N. / Kereiche, S. / Pinkas, M. / Krajcovicova, V. / Bauer, J.A. / Stojkovicova, B. / Havalova, H. / Lukacova, V. / Kohutova, L. / Martinakova, L. / Barath, P. / ...Authors: Ondrovicova, G. / Kunova, N. / Kereiche, S. / Pinkas, M. / Krajcovicova, V. / Bauer, J.A. / Stojkovicova, B. / Havalova, H. / Lukacova, V. / Kohutova, L. / Martinakova, L. / Barath, P. / Novacek, J. / Kutejova, E. / Pevala, V.
History
DepositionMar 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lon protease homolog, mitochondrial
B: Lon protease homolog, mitochondrial
C: Lon protease homolog, mitochondrial
D: Lon protease homolog, mitochondrial
E: Lon protease homolog, mitochondrial
F: Lon protease homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)591,55812
Polymers588,9956
Non-polymers2,5636
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area37800 Å2
ΔGint-120 kcal/mol
Surface area220870 Å2

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Components

#1: Protein
Lon protease homolog, mitochondrial / LONHs / Lon protease-like protein / LONP / Mitochondrial ATP-dependent protease Lon / Serine protease 15


Mass: 98165.789 Da / Num. of mol.: 6 / Mutation: Y394E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LONP1, PRSS15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: P36776, endopeptidase La
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human mitochondrial Lon protease / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organelle: mitochondria
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta 2(DE3)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.21rc1_4895 / Classification: refinement
EM softwareName: PHENIX / Version: 1.21rc1_4895 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 367678 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7NFY

7nfy


Pdb chain-ID: A / Accession code: 7NFY / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 187.87 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00237662
ELECTRON MICROSCOPYf_angle_d0.504550874
ELECTRON MICROSCOPYf_chiral_restr0.03845838
ELECTRON MICROSCOPYf_plane_restr0.00346534
ELECTRON MICROSCOPYf_dihedral_angle_d5.19175124

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