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- EMDB-36977: CryoEM structure of LonC protease hexamer with Bortezomib -

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Basic information

Entry
Database: EMDB / ID: EMD-36977
TitleCryoEM structure of LonC protease hexamer with Bortezomib
Map dataCryoEM map of LonC hexamer with Bortezomib
Sample
  • Complex: CryoEM structure of LonC protease hexamer with Bortezomib
    • Protein or peptide: endopeptidase La
  • Ligand: PHOSPHATE ION
  • Ligand: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
KeywordsLon proteases / chaperone / hexamer / 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
Biological speciesMeiothermus taiwanensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsLi M / Hsieh K / Liu H / Zhang S / Gao Y / Gong Q / Zhang K / Chang C / Li S
Funding support China, 1 items
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 KY / Zhang S / Gao Y / Gong Q / Zhang K / Chang CI / Li S
History
DepositionJul 31, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36977.png

Downloads & links

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Map

FileDownload / File: emd_36977.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of LonC hexamer with Bortezomib
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.61328906 - 0.9950834
Average (Standard dev.)0.0007202046 (±0.034298833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoEM map of LonC hexamer with Bortezomib

Fileemd_36977_additional_1.map
AnnotationCryoEM map of LonC hexamer with Bortezomib
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM map of LonC hexamer with Bortezomib

Fileemd_36977_half_map_1.map
AnnotationCryoEM map of LonC hexamer with Bortezomib
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM map of LonC hexamer with Bortezomib

Fileemd_36977_half_map_2.map
AnnotationCryoEM map of LonC hexamer with Bortezomib
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of LonC protease hexamer with Bortezomib

EntireName: CryoEM structure of LonC protease hexamer with Bortezomib
Components
  • Complex: CryoEM structure of LonC protease hexamer with Bortezomib
    • Protein or peptide: endopeptidase La
  • Ligand: PHOSPHATE ION
  • Ligand: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE

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Supramolecule #1: CryoEM structure of LonC protease hexamer with Bortezomib

SupramoleculeName: CryoEM structure of LonC protease hexamer with Bortezomib
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Meiothermus taiwanensis (bacteria)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: endopeptidase La

MacromoleculeName: endopeptidase La / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: endopeptidase La
Source (natural)Organism: Meiothermus taiwanensis (bacteria)
Molecular weightTheoretical: 80.558352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLSYEALEW RTPIENSTEP VSLPPPPPFF GQERAREALE LAIRGGFHAY LVGPPSLGKH EALLAYLSTQ SVETPPDLLY VPLSERKVA VLTLPSGQEI HLAEAVEGLL LEVNRLDELF RQGSFLREKT QLEARFKEAR EQQLEALRRE AQEAGFALST N GERLELTG ...String:
MRLSYEALEW RTPIENSTEP VSLPPPPPFF GQERAREALE LAIRGGFHAY LVGPPSLGKH EALLAYLSTQ SVETPPDLLY VPLSERKVA VLTLPSGQEI HLAEAVEGLL LEVNRLDELF RQGSFLREKT QLEARFKEAR EQQLEALRRE AQEAGFALST N GERLELTG PGPVPAELSA RLEEVTLGSL AASAELEVAL RRLRRDWALH YLNNRFEPLF QRFPQARAYL EALRARLARY AE TGEPLDP AQWRPNLLTS SSSGTPPPIV YEPYATAPRL FGRLDYLVDR GVWSTNVSLI RPGAVHRAQG GYLILDALSL KRE GTWEAF KRALRNGQVE PVTEPQAPAG LEVEPFPIQM QVILVGTPEA FEGLEEDPAF SELFRIRAEF SPTLPASPEN CTAL GGWLL AQGFQLTQGG LTRLYDEARR MAEQRDRMDA RLVEIRALAE EAAVLGGGLL TAESVEQAIA AREHRSFLSE EEFLR AVQE GVIRLRTTGR AVGEVNSLVV VEAAPYWGRP ARLTARAAPG RDHLISIDRE AGLGGQIFHK AVLTLAGYLR SRYIEH GSL PVTISLAFEQ NYVSIEGDSA GLAELVAALS AIGNLPLRQD LAVTGAVDQT GKVLAVGAIN AKVEGFFRVC KALGLSG TQ GVILPEANLA NLTLRAEVLE AVRAGQFHIY AVETAEQALE ILAGARMEGF RGLQEKIRAG LEAFARLEEG HDKEDREK L AAALEHHHHH H

UniProtKB: endopeptidase La

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Macromolecule #2: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #3: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL...

MacromoleculeName: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
type: ligand / ID: 3 / Number of copies: 6 / Formula: BO2
Molecular weightTheoretical: 384.237 Da
Chemical component information

ChemComp-BO2:
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / medication, anticancer*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

Concentration1.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3189167
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 387608
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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