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- PDB-7fd4: A complete three-dimensional structure of the Lon protease transl... -

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Basic information

Entry
Database: PDB / ID: 7fd4
TitleA complete three-dimensional structure of the Lon protease translocating a protein substrate (conformation 1)
Components
  • Alpha-S1-casein
  • Lon proteaseLon protease family
KeywordsHYDROLASE/PROTEIN BINDING / AAA+ protease / Lon / complete three-dimensional structure / N-terminal domain / CYTOSOLIC PROTEIN / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


endopeptidase La / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Lon protease, bacterial / Peptidase S16, active site / Lon protease, bacterial/eukaryotic-type / ATP-dependent serine proteases, lon family, serine active site. / Lon protease (S16) C-terminal proteolytic domain / Lon protease / Peptidase S16, Lon proteolytic domain / Lon proteolytic domain profile. / Lon N-terminal domain profile. / Found in ATP-dependent protease La (LON) ...Lon protease, bacterial / Peptidase S16, active site / Lon protease, bacterial/eukaryotic-type / ATP-dependent serine proteases, lon family, serine active site. / Lon protease (S16) C-terminal proteolytic domain / Lon protease / Peptidase S16, Lon proteolytic domain / Lon proteolytic domain profile. / Lon N-terminal domain profile. / Found in ATP-dependent protease La (LON) / Lon, substrate-binding domain / ATP-dependent protease La (LON) substrate-binding domain / 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
Chem-4KZ / ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Lon protease
Similarity search - Component
Biological speciesMeiothermus taiwanensis (bacteria)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLi, S. / Hsieh, K. / Kuo, C. / Lee, S. / Pintilie, G. / Zhang, K. / Chang, C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2320-B-001-011-MY3 Taiwan
CitationJournal: Sci Adv / Year: 2021
Title: Complete three-dimensional structures of the Lon protease translocating a protein substrate.
Authors: Shanshan Li / Kan-Yen Hsieh / Chiao-I Kuo / Szu-Hui Lee / Grigore D Pintilie / Kaiming Zhang / Chung-I Chang /
Abstract: [Figure: see text].
History
DepositionJul 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
B: Lon protease
C: Lon protease
D: Lon protease
E: Lon protease
F: Lon protease
A: Lon protease
S: Alpha-S1-casein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)538,67519
Polymers533,2187
Non-polymers5,45712
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Lon protease / Lon protease family / ATP-dependent protease La


Mass: 88554.594 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Gene: lonA1, lon / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059VAZ3, endopeptidase La
#2: Protein/peptide Alpha-S1-casein


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-4KZ / N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide


Mass: 418.253 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H23BN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Sequence detailsAuthors know the sequence of chain S (UNP P02662) but don't know how the coordinates align with the ...Authors know the sequence of chain S (UNP P02662) but don't know how the coordinates align with the sequence. P02662 sequence is MKLLILTCLV AVALARPKHP IKHQGLPQEV LNENLLRFFV APFPEVFGKE KVNELSKDIG SESTEDQAME DIKQMEAESI SSSEEIVPNS VEQKHIQKED VPSERYLGYL EQLLRLKKYK VPQLEIVPNS AEERLHSMKE GIHAQQKEPM IGVNQELAYF YPELFRQFYQ LDAYPSGAWY YVPLGTQYTD APSFSDIPNP IGSENSEKTT MPLW

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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

Component
IDNameTypeEntity IDParent-IDSource
1A complete three-dimensional structure of the Lon protease translocating a protein substrate (conformation 1)COMPLEX#1-#20MULTIPLE SOURCES
2Lon proteaseLon protease familyCOMPLEX#11RECOMBINANT
3Alpha-S1-caseinCOMPLEX#21NATURAL
Molecular weightValue: 0.37 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Meiothermus taiwanensis (bacteria)172827
32Bos taurus (cattle)9913
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.5 mg/ml / Embedding 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: 48 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158553 / Symmetry type: POINT

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