+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12316 | |||||||||
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Title | D1-state of wild type human mitochondrial LONP1 protease | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human mitochondrial AAA+ protease / MOTOR PROTEIN | |||||||||
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 / protein catabolic process / ADP binding / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.0 Å | |||||||||
Authors | Mohammed I / Schmitz KA | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12316.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-12316-v30.xml emd-12316.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_12316.png | 52.3 KB | ||
Filedesc metadata | emd-12316.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12316 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12316 | HTTPS FTP |
-Validation report
Summary document | emd_12316_validation.pdf.gz | 456 KB | Display | EMDB validaton report |
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Full document | emd_12316_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | emd_12316_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_12316_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12316 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12316 | HTTPS FTP |
-Related structure data
Related structure data | 7ngpMC 7nfyC 7ng4C 7ng5C 7ngcC 7ngfC 7nglC 7ngqC 7oxoC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12316.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.6531 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : D1-state of LonP1 hexameric complex
Entire | Name: D1-state of LonP1 hexameric complex |
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Components |
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-Supramolecule #1: D1-state of LonP1 hexameric complex
Supramolecule | Name: D1-state of LonP1 hexameric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 600 KDa |
-Macromolecule #1: Lon protease homolog, mitochondrial
Macromolecule | Name: Lon protease homolog, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: endopeptidase La |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 93.201383 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: HLPLIAITRN PVFPRFIKII EVKNKKLVEL LRRKVRLAQP YVGVFLKRDD SNESDVVESL DEIYHTGTFA QIHEMQDLGD KLRMIVMGH RRVHISRQLE VEPEEPEAEN KHKPRRKSKR GKKEAEDELS ARHPAELAME PTPELPAEVL MVEVENVVHE D FQVTEEVK ...String: HLPLIAITRN PVFPRFIKII EVKNKKLVEL LRRKVRLAQP YVGVFLKRDD SNESDVVESL DEIYHTGTFA QIHEMQDLGD KLRMIVMGH RRVHISRQLE VEPEEPEAEN KHKPRRKSKR GKKEAEDELS ARHPAELAME PTPELPAEVL MVEVENVVHE D FQVTEEVK ALTAEIVKTI RDIIALNPLY RESVLQMMQA GQRVVDNPIY LSDMGAALTG AESHELQDVL EETNIPKRLY KA LSLLKKE FELSKLQQRL GREVEEKIKQ THRKYLLQEQ LKIIKKELGL EKDDKDAIEE KFRERLKELV VPKHVMDVVD EEL SKLGLL DNHSSEFNVT RNYLDWLTSI PWGKYSNENL DLARAQAVLE EDHYGMEDVK KRILEFIAVS QLRGSTQGKI LCFY GPPGV GKTSIARSIA RALNREYFRF SVGGMTDVAE IKGHRRTYVG AMPGKIIQCL KKTKTENPLI LIDEVDKIGR GYQGD PSSA LLELLDPEQN ANFLDHYLDV PVDLSKVLFI CTANVTDTIP EPLRDRMEMI NVSGYVAQEK LAIAERYLVP QARALC GLD ESKAKLSSDV LTLLIKQYCR ESGVRNLQKQ VEKVLRKSAY KIVSGEAESV EVTPENLQDF VGKPVFTVER MYDVTPP GV VMGLAWTAMG GSTLFVETSL RRPQDKDAKG DKDGSLEVTG QLGEVMKESA RIAYTFARAF LMQHAPANDY LVTSHIHL H VPEGATPKDG PSAGCTIVTA LLSLAMGRPV RQNLAMTGEV SLTGKILPVG GIKEKTIAAK RAGVTCIVLP AENKKDFYD LAAFITEGLE VHFVEHYREI FDIAFP UniProtKB: Lon protease homolog, mitochondrial |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.45 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE Details: ab-initio; The coordinates of 7ngl subunits, including bound nucleotides, were fitted as rigid bodies into the low resolution density of the LonP1 D1-state. The N-domains (res. 123-410) were ...Details: ab-initio; The coordinates of 7ngl subunits, including bound nucleotides, were fitted as rigid bodies into the low resolution density of the LonP1 D1-state. The N-domains (res. 123-410) were fitted separately from the combined A- and protease domains (res 411-1001). The connecting loops (res 405-415) were reconnected with good geometry. Clashes between the rigid bodies were not corrected due to the low resolution. |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 15000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7ngp: |