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- EMDB-34000: Open-spiral pentamer of the substrate-free Lon protease with a Y2... -

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Basic information

Entry
Database: EMDB / ID: EMD-34000
TitleOpen-spiral pentamer of the substrate-free Lon protease with a Y224S mutation
Map dataPentameric state of MtaLon-Y224S with ATPgammaS
Sample
  • Complex: Homo-pentameric complex of Lon protease with ATPgammaS
    • Protein or peptide: Lon protease
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsLon protease / hydrolysis / AAA proteins / HYDROLASE
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Lon protease, bacterial / : / 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, bacterial / : / 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
Biological speciesMeiothermus taiwanensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsLi S / Hsieh KY / Kuo CI / Lee SH / Ho MR / Wang CH / Zhang K / Chang CI
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2320-B-001-011-MY3 Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: A 5+1 assemble-to-activate mechanism of the Lon proteolytic machine.
Authors: Shanshan Li / Kan-Yen Hsieh / Chiao-I Kuo / Tzu-Chi Lin / Szu-Hui Lee / Yi-Ru Chen / Chun-Hsiung Wang / Meng-Ru Ho / See-Yeun Ting / Kaiming Zhang / Chung-I Chang /
Abstract: Many AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In ...Many AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In this ATP-dependent translocating state, the substrate is gripped by the pore loops of the ATPase domains arranged in a universal right-handed spiral staircase organization. However, the process by which a AAA+ protein is activated to adopt this substrate-pore-loop arrangement remains unknown. We show here, using cryo-electron microscopy (cryo-EM), that the activation process of the Lon AAA+ protease may involve a pentameric assembly and a substrate-dependent incorporation of the sixth protomer to form the substrate-pore-loop contacts seen in the translocating state. Based on the structural results, we design truncated monomeric mutants that inhibit Lon activity by binding to the native pentamer and demonstrated that expressing these monomeric mutants in Escherichia coli cells containing functional Lon elicits specific phenotypes associated with lon deficiency, including the inhibition of persister cell formation. These findings uncover a substrate-dependent assembly process for the activation of a AAA+ protein and demonstrate a targeted approach to selectively inhibit its function within cells.
History
DepositionAug 3, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34000.png

Downloads & links

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Map

FileDownload / File: emd_34000.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPentameric state of MtaLon-Y224S with ATPgammaS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.13022685 - 0.27585933
Average (Standard dev.)0.00020675191 (±0.008289858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_34000_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_34000_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homo-pentameric complex of Lon protease with ATPgammaS

EntireName: Homo-pentameric complex of Lon protease with ATPgammaS
Components
  • Complex: Homo-pentameric complex of Lon protease with ATPgammaS
    • Protein or peptide: Lon protease
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: Homo-pentameric complex of Lon protease with ATPgammaS

SupramoleculeName: Homo-pentameric complex of Lon protease with ATPgammaS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Meiothermus taiwanensis (bacteria)
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: Lon protease

MacromoleculeName: Lon protease / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: endopeptidase La
Source (natural)Organism: Meiothermus taiwanensis (bacteria)
Molecular weightTheoretical: 88.478492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLELPVIPL RNTVILPHTT TPVDVGRAKS KRAVEEAMGA DRLIFLVAQR DPEVDDPAPD DLYTWGVQAV VKQAMRLPDG TLQVMVEAR ARAQVTDYIP GPYLRARGEV FSEIFPIDEA VVRVLVEELK EAFEKYVANH KSLRLDRYQL EAVKGTSDPA M LADTIAYH ...String:
MRLELPVIPL RNTVILPHTT TPVDVGRAKS KRAVEEAMGA DRLIFLVAQR DPEVDDPAPD DLYTWGVQAV VKQAMRLPDG TLQVMVEAR ARAQVTDYIP GPYLRARGEV FSEIFPIDEA VVRVLVEELK EAFEKYVANH KSLRLDRYQL EAVKGTSDPA M LADTIAYH ATWTVAEKQE ILELTDLEAR LKKVLGLLSR DLERFELDKR VAQRVKEQMD TNQRESYLRE QMKAIQKELG GE DGLSDLE ALRKKIEEVG MPEAVKTKAL KELDRLERMQ QGSPEATVAR TYLDWLTEVP WSKADPEVLD INHTRQVLDE DHY GLKDVK ERILEYLAVR QLTQGLDVRN KAPILVLVGP PGVGKTSLGR SIARSMNRKF HRISLGGVRD EAEIRGHRRT YIGA MPGKL IHAMKQVGVI NPVILLDEID KMSSDWRGDP ASAMLEVLDP EQNNTFTDHY LDVPYDLSKV FFITTANTLQ TIPRP LLDR MEVIEIPGYT NMEKQAIARQ YLWPKQVRES GMEGRIEVTD AAILRVISEY TREAGVRGLE RELGKIARKG AKFWLE GAW EGLRTIDASD IPTYLGIPRY RPDKAETEPQ VGTAQGLAWT PVGGTLLTIE VAAVPGSGKL SLTGQLGEVM KESAQAA LT YLRAHTQDYG LPEDFYNKVD LHVHVPDGAT PKDGPSAGIT MATAIASALS RRPARMDIAM TGEVSLRGKV MPIGGVKE K LLAAHQAGIH KIVLPKDNEA QLEELPKEVL EGLEIKLVED VGEVLEYLLL PEPTMPPVVQ PSDNRQQPGA GA

UniProtKB: Lon protease

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Macromolecule #2: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mM(HOCH2)3CNH2tris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
10.0 mMMgCl2magnesium chloride
1.0 mMC4H10O2S2dithiothreitol
2.0 mMC10H16N5O12P3SLiAdenosine- 5'- O- (3- thiotriphosphate)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K
DetailsMtaLon-Y224S was incubated with ATPgammaS

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 12982 / Average exposure time: 1.34 sec. / Average electron dose: 73.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4721627
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 777117
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.2)

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