+Open data
-Basic information
Entry | Database: PDB / ID: 8om7 | ||||||||||||||||||||||||
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Title | Human Mitochondrial Lon Y186E Mutant ADP Bound | ||||||||||||||||||||||||
Components | Lon protease homolog, mitochondrial | ||||||||||||||||||||||||
Keywords | HYDROLASE / 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 | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å | ||||||||||||||||||||||||
Authors | Kereiche, S. / Bauer, J.A. / Matyas, P. / Novacek, J. / Kutejova, E. | ||||||||||||||||||||||||
Funding support | European Union, Czech Republic, 7items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8om7.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8om7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8om7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/8om7 ftp://data.pdbj.org/pub/pdb/validation_reports/om/8om7 | HTTPS FTP |
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-Related structure data
Related structure data | 16970MC 8okaC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 98165.789 Da / Num. of mol.: 6 / Mutation: Y186E 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 / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human mitochondrial Lon protease / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) / Organelle: mitochondria |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Rosetta 2(DE3) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.21rc1_4895 / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: PHENIX / Version: 1.21rc1_4895 / Category: model refinement | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39948 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7NFY Pdb chain-ID: A / Accession code: 7NFY / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 314.81 Å2 | ||||||||||||||||||||||||
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