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- PDB-7p0b: Human mitochondrial Lon protease without substrate -

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Basic information

Entry
Database: PDB / ID: 7p0b
TitleHuman mitochondrial Lon protease without substrate
ComponentsLon protease homolog, mitochondrial
KeywordsHYDROLASE / Protease / Mitochondria / AAA+
Function / homology
Function and homology information


oxidation-dependent protein catabolic process / response to aluminum ion / PH domain binding / endopeptidase La / mitochondrial protein catabolic process / mitochondrial DNA metabolic process / G-quadruplex DNA binding / : / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins ...oxidation-dependent protein catabolic process / response to aluminum ion / PH domain binding / endopeptidase La / mitochondrial protein catabolic process / mitochondrial DNA metabolic process / G-quadruplex DNA binding / : / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid / insulin receptor substrate binding / Mitochondrial unfolded protein response (UPRmt) / chaperone-mediated protein complex assembly / response to hormone / DNA polymerase binding / Mitochondrial protein degradation / negative regulation of insulin receptor signaling pathway / 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 / response to hypoxia / single-stranded RNA binding / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Lon protease homologue, chloroplastic/mitochondrial / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / 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 homologue, chloroplastic/mitochondrial / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / 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 N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / 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: 4.11 Å
AuthorsValentin Gese, G. / Shahzad, S. / Hallberg, B.M.
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 11, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model / refine
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _refine.ls_d_res_high / _refine.ls_d_res_low
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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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)594,54812
Polymers591,9856
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area27140 Å2
ΔGint-102 kcal/mol
Surface area125570 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: 98664.133 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


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

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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 LonP1 G106P, R563W and K594M mutant
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.591 MDa / Experimental 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
7Coot0.93model fitting
19REFMAC5.8.0267model refinement
20PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61980 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 3M6A

3m6a


Pdb chain-ID: A / Accession code: 3M6A / Source name: PDB / Type: experimental model
RefinementResolution: 4.11→4.11 Å / Cor.coef. Fo:Fc: 0.951 / WRfactor Rwork: 0.287 / SU B: 54.458 / SU ML: 0.651 / Average fsc overall: 0.7665 / Average fsc work: 0.7665 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.2869 70778 -
all0.287 --
Rfree--0 %
obs--99.944 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 260.869 Å2
Baniso -1Baniso -2Baniso -3
1--4.364 Å23.115 Å21.674 Å2
2--2.721 Å27.294 Å2
3---1.643 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0040.01225506
ELECTRON MICROSCOPYr_angle_refined_deg1.1991.63734541
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.36753172
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.56822.3281267
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.892154553
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.46215168
ELECTRON MICROSCOPYr_chiral_restr0.0960.23334
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.0218958
ELECTRON MICROSCOPYr_nbd_refined0.1830.224702
ELECTRON MICROSCOPYr_nbtor_refined0.2830.235732
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1390.21460
ELECTRON MICROSCOPYr_mcbond_it15.10525.11612727
ELECTRON MICROSCOPYr_mcangle_it25.9937.63315886
ELECTRON MICROSCOPYr_scbond_it17.2926.93912779
ELECTRON MICROSCOPYr_scangle_it29.67839.80618655
ELECTRON MICROSCOPYr_lrange_it52.889484.465104669
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
4-4.1031.21352191.21352190.1391.213
4.103-4.2150.88850810.88850810.3680.888
4.215-4.3360.59749310.59749310.5760.597
4.336-4.4690.41547990.41547990.7010.415
4.469-4.6140.34346030.34346030.7990.343
4.614-4.7740.31645740.31645740.8510.316
4.774-4.9530.30642840.30642840.8810.306
4.953-5.1530.2941970.2941970.8790.29
5.153-5.3790.28539870.28539870.8740.285
5.379-5.6390.26638590.26638590.8930.266
5.639-5.940.26936320.26936320.8930.269
5.94-6.2940.27634580.27634580.8930.276
6.294-6.7210.24932060.24932060.9120.249
6.721-7.2490.23230850.23230850.9390.232
7.249-7.9240.23727460.23727460.9390.237
7.924-8.8320.24925480.24925480.9510.249
8.832-10.1460.23222300.23222300.9630.232
10.146-12.30.18519140.18519140.970.185
12.3-16.8910.18814870.18814870.9690.188
16.891-50.0050.3229120.3229120.9820.322

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