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- PDB-7ngq: Human mitochondrial Lon protease homolog, D2-state -

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Basic information

Entry
Database: PDB / ID: 7ngq
TitleHuman mitochondrial Lon protease homolog, D2-state
ComponentsLon protease homolog, mitochondrial
KeywordsMOTOR PROTEIN / protease / unfolds / hexamer / AAA+ 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 / response to hormone / proteolysis involved in protein catabolic process / 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: 12 Å
AuthorsMohammed, I. / Abrahams, J.P. / Schmitz, K.A. / Maier, T. / Schenck, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_165669 Switzerland
CitationJournal: 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
DepositionFeb 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 2.0Jul 7, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Data processing / Database references / Derived calculations / Experimental preparation / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / audit_author / cell / citation / citation_author / em_3d_fitting / em_3d_fitting_list / em_3d_reconstruction / em_buffer / em_entity_assembly / em_entity_assembly_molwt / em_entity_assembly_recombinant / em_image_recording / em_imaging / em_single_particle_entity / em_software / em_specimen / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine_ls_restr / software / struct / struct_conf / struct_conn / struct_keywords / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _audit_author.name / _citation.title ..._audit_author.name / _citation.title / _citation_author.name / _em_3d_fitting.details / _em_3d_fitting.overall_b_value / _em_3d_fitting.ref_space / _em_3d_fitting.target_criteria / _em_3d_reconstruction.resolution / _em_buffer.pH / _em_entity_assembly.name / _em_entity_assembly_molwt.experimental_flag / _em_entity_assembly_molwt.units / _em_entity_assembly_molwt.value / _em_entity_assembly_recombinant.ncbi_tax_id / _em_entity_assembly_recombinant.organism / _em_image_recording.avg_electron_dose_per_image / _em_image_recording.detector_mode / _em_imaging.illumination_mode / _em_specimen.concentration / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_assembly_prop.value / _struct.title / _struct_keywords.text
Provider: author / Type: Coordinate replacement
Revision 2.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.3Nov 9, 2022Group: Database references / Category: citation / Item: _citation.page_last

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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)561,77212
Polymers559,2086
Non-polymers2,5636
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28920 Å2
ΔGint-71 kcal/mol
Surface area237650 Å2
MethodPISA

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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: 93201.383 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LONP1, PRSS15 / Production host: Escherichia coli (E. coli) / 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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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: Lon protease homolog, mitochondrial / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
7Cootmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11000 / Symmetry type: POINT
Atomic model buildingB value: 850 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Details: The coordinates of 7ngl subunits were fitted as rigid bodies into the low resolution density of the LonP1 D2-state. The N-domains (res. 123-410) were fitted separately from the combined A- ...Details: The coordinates of 7ngl subunits were fitted as rigid bodies into the low resolution density of the LonP1 D2-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.
Atomic model buildingPDB-ID: 7NGL

7ngl

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