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- PDB-8k96: CryoEM structure of LonC protease hepatmer with Bortezomib -

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Basic information

Entry
Database: PDB / ID: 8k96
TitleCryoEM structure of LonC protease hepatmer with Bortezomib
Componentsendopeptidase La
KeywordsCHAPERONE / Lon proteases / hepatmer / inhibitor
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding
Similarity search - Function
Lon protease, AAA domain / LonB-like, AAA domain / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-BO2 / PHOSPHATE ION / endopeptidase La
Similarity search - Component
Biological speciesMeiothermus taiwanensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsLi, M. / Hsieh, K. / Liu, H. / Zhang, S. / Gao, Y. / Gong, Q. / Zhang, K. / Chang, C. / Li, S.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Fundam Res / Year: 2024
Title: Bifurcated assembly pathway and dual function of a Lon-like protease revealed by cryo-EM Analysis
Authors: Li, M. / Liu, H. / Hsieh, K.Y. / Zhang, S. / Gao, Y. / Gong, Q. / Zhang, K. / Chang, C.I. / Li, S.
History
DepositionJul 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin ...citation / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: endopeptidase La
A: endopeptidase La
G: endopeptidase La
F: endopeptidase La
E: endopeptidase La
D: endopeptidase La
C: endopeptidase La
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,26321
Polymers563,9087
Non-polymers3,35414
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
endopeptidase La / LonC protease


Mass: 80558.352 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Gene: lon_2, Mcate_02721 / Production host: Escherichia coli (E. coli) / References: UniProt: C9DRU9, endopeptidase La
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB


Mass: 384.237 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer*YM
Has ligand of interestY
Has protein modificationY

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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: CryoEM structure of LonC protease hepatmer with Bortezomib
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.56 MDa / Experimental value: YES
Source (natural)Organism: Meiothermus taiwanensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 1 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 FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
12cryoSPARC3.2classification
13cryoSPARC3.23D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3189167
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154341 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00240047
ELECTRON MICROSCOPYf_angle_d0.5454369
ELECTRON MICROSCOPYf_dihedral_angle_d4.6215768
ELECTRON MICROSCOPYf_chiral_restr0.0396041
ELECTRON MICROSCOPYf_plane_restr0.0047259

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