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- PDB-6wzv: Lon protease proteolytic domain -

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Basic information

Entry
Database: PDB / ID: 6wzv
TitleLon protease proteolytic domain
ComponentsLon protease homolog, mitochondrial
KeywordsHYDROLASE / proteolytic domain
Function / homology
Function and homology information


oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / response to aluminum ion / endopeptidase La / G-quadruplex DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins ...oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / response to aluminum ion / endopeptidase La / G-quadruplex DNA binding / 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 / Mitochondrial unfolded protein response (UPRmt) / chaperone-mediated protein complex assembly / DNA polymerase binding / response to hormone / 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) / Ribosomal Protein S5; domain 2 - #10 / PUA-like superfamily / Ribosomal Protein S5; domain 2 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-UFY / Lon protease homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsLee, C.C. / Spraggon, G.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Design of Selective LONP1 Inhibitors for Probing In Vitro Biology.
Authors: Kingsley, L.J. / He, X. / McNeill, M. / Nelson, J. / Nikulin, V. / Ma, Z. / Lu, W. / Zhou, V.W. / Manuia, M. / Kreusch, A. / Gao, M.Y. / Witmer, D. / Vaillancourt, M.T. / Lu, M. / ...Authors: Kingsley, L.J. / He, X. / McNeill, M. / Nelson, J. / Nikulin, V. / Ma, Z. / Lu, W. / Zhou, V.W. / Manuia, M. / Kreusch, A. / Gao, M.Y. / Witmer, D. / Vaillancourt, M.T. / Lu, M. / Greenblatt, S. / Lee, C. / Vashisht, A. / Bender, S. / Spraggon, G. / Michellys, P.Y. / Jia, Y. / Haling, J.R. / Lelais, G.
History
DepositionMay 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,5179
Polymers71,3653
Non-polymers1,1536
Water1,51384
1
A: Lon protease homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3654
Polymers23,7881
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lon protease homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2693
Polymers23,7881
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lon protease homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8842
Polymers23,7881
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.276, 186.276, 159.718
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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: 23788.221 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LONP1, PRSS15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36776, endopeptidase La
#2: Chemical ChemComp-UFY / N-[(1R)-1-borono-3-methylbutyl]-Nalpha-(pyrazine-2-carbonyl)-D-phenylalaninamide


Mass: 384.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 1.6M ammonium sulfate, 0.1M Bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2017 / Details: Mirror: Rh coated flat
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 35939 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.066 / Rrim(I) all: 0.127 / Χ2: 1.359 / Net I/σ(I): 6.8 / Num. measured all: 127739
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.51-2.573.31.38825480.3490.8781.650.46499.5
2.57-2.643.51.09525720.4450.6721.290.47999.9
2.64-2.723.60.87925520.7990.5321.0310.50399.5
2.72-2.813.60.64125760.7480.3830.7490.50999.4
2.81-2.913.40.45925700.8510.2840.5420.55399.4
2.91-3.023.50.30725370.9220.1870.3610.60598.6
3.02-3.163.70.24325710.9470.1440.2840.66799.3
3.16-3.333.70.18425630.9640.1090.2140.87899.7
3.33-3.543.60.1425400.9740.0850.1641.29398.8
3.54-3.813.50.10925760.9820.0670.1281.8899
3.81-4.193.70.09425770.9870.0560.112.39999.3
4.19-4.83.40.07525610.9890.0460.0882.99797.5
4.8-6.053.70.07625830.9910.0450.0892.91398.8
6.05-503.40.05326130.9970.0320.0622.82996.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WYS

6wys


Resolution: 2.51→39.1 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2139 1824 5.08 %
Rwork0.1768 34108 -
obs0.1786 35932 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.94 Å2 / Biso mean: 69.4967 Å2 / Biso min: 32.68 Å2
Refinement stepCycle: final / Resolution: 2.51→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4249 0 76 84 4409
Biso mean--75.64 60.93 -
Num. residues----574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.580.35931280.30522561268997
2.58-2.650.32561590.283926212780100
2.65-2.740.28751230.26242641276499
2.74-2.840.28361410.23262604274599
2.84-2.950.29471500.21212601275199
2.95-3.090.23451460.20322621276799
3.09-3.250.26551300.20832628275899
3.25-3.450.23891500.1982628277899
3.45-3.720.22841480.17052611275999
3.72-4.090.19411390.14882641278099
4.09-4.680.15461400.12392611275198
4.68-5.890.16811300.15692658278898
5.9-39.10.19571400.17092682282297
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7019-1.0409-3.21753.83023.09076.3344-0.0039-0.3175-0.27290.0339-0.0442-0.1816-0.23430.34780.00580.3166-0.03770.02220.48440.15080.423430.126328.05861.8203
23.88340.51120.22757.1969-2.94051.88260.08110.4901-0.1195-0.45620.16460.28340.7124-0.8846-0.14070.5161-0.02890.02710.57770.00040.461516.6031325.516256.1707
35.41592.7544-0.72922.6278-2.47174.1333-0.0370.59850.5984-0.74090.28510.38710.3695-0.3135-0.32150.5589-0.00890.02850.62720.09910.598117.9385337.507453.6085
42.53821.2876-0.88156.1882-2.7796.54260.04580.31460.1295-0.5636-0.0447-0.14120.5104-0.04380.08480.314-0.00840.05420.50480.06060.434521.3322329.236955.3585
51.6323-0.1751.3981.44480.211.89290.1344-0.0430.2631-0.0732-0.0772-0.4268-0.2190.5817-0.04980.4133-0.07960.04720.55410.0950.479829.9718337.931460.9574
63.53870.41221.51672.53031.20438.72510.05740.22950.0728-0.14920.1049-0.2977-0.62730.568-0.07080.4158-0.17030.06790.47110.10960.564834.4301345.717365.0848
74.7753-2.6853-4.33212.15163.96897.6022-0.61660.3928-0.1681-2.0396-0.0436-1.9053-0.1468-1.30650.00730.9115-0.00650.38160.97230.16380.875239.3121343.100142.9543
83.80173.39562.91228.38995.64034.0138-0.0264-0.3096-0.41810.13410.0206-0.16180.46840.06410.0350.43030.11990.11740.49190.04460.561921.0699298.432463.1945
94.4356-0.5687-0.92495.49360.697.043-0.12410.45430.2817-0.69440.1191-0.07550.10270.1330.03270.4375-0.01140.0530.38750.0010.327218.2418312.707853.6049
106.82972.8641-0.83923.7587-0.32425.2979-0.08240.6248-0.2854-0.35570.0898-0.0463-0.1383-0.1640.06540.40060.07750.05740.3777-0.00990.461116.4469307.353655.3359
111.5379-0.49860.62260.7633-1.48742.1487-0.06730.1835-0.4347-0.06320.0823-0.16540.40080.43810.00910.4690.07930.11150.61-0.01860.524628.2757304.136961.1751
124.3439-0.44262.66232.2302-2.62129.35760.08330.1796-0.3162-0.0707-0.1174-0.38590.72920.72760.12220.39970.12570.10510.65890.00420.627136.7738304.072163.7994
130.5459-0.27030.264.8272-1.09970.50570.0671-0.081-0.72740.54040.2720.19160.1422-0.1569-0.32510.59930.03370.16560.81840.18870.747543.5705320.159150.3505
143.6481-2.3153-0.84735.6503-0.12817.62970.56570.71111.1163-1.0535-0.0075-0.129-0.7792-0.5618-0.54270.7930.10210.2750.81530.28220.703142.3419335.200231.9593
152.79-2.69390.97192.78560.05243.75940.37490.42390.4881-0.1233-0.2443-0.3739-0.28730.1946-0.17460.5625-0.0560.18940.68960.17510.569848.3854326.412438.1046
164.8326-2.65864.4973.6265-0.99236.34850.37480.4164-0.2746-0.5697-0.0225-0.04950.4459-0.0857-0.24430.73710.03340.16220.73330.02880.454352.961316.031636.098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 754 through 786 )A754 - 786
2X-RAY DIFFRACTION2chain 'A' and (resid 787 through 807 )A787 - 807
3X-RAY DIFFRACTION3chain 'A' and (resid 808 through 828 )A808 - 828
4X-RAY DIFFRACTION4chain 'A' and (resid 829 through 856 )A829 - 856
5X-RAY DIFFRACTION5chain 'A' and (resid 857 through 908 )A857 - 908
6X-RAY DIFFRACTION6chain 'A' and (resid 909 through 946 )A909 - 946
7X-RAY DIFFRACTION7chain 'A' and (resid 947 through 957 )A947 - 957
8X-RAY DIFFRACTION8chain 'B' and (resid 754 through 784 )B754 - 784
9X-RAY DIFFRACTION9chain 'B' and (resid 785 through 828 )B785 - 828
10X-RAY DIFFRACTION10chain 'B' and (resid 829 through 856 )B829 - 856
11X-RAY DIFFRACTION11chain 'B' and (resid 857 through 908 )B857 - 908
12X-RAY DIFFRACTION12chain 'B' and (resid 909 through 949 )B909 - 949
13X-RAY DIFFRACTION13chain 'C' and (resid 745 through 773 )C745 - 773
14X-RAY DIFFRACTION14chain 'C' and (resid 774 through 839 )C774 - 839
15X-RAY DIFFRACTION15chain 'C' and (resid 840 through 908 )C840 - 908
16X-RAY DIFFRACTION16chain 'C' and (resid 909 through 948 )C909 - 948

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