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- EMDB-36978: CryoEM map of LonC protease open hexamer with Bortezomib -

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Basic information

Entry
Database: EMDB / ID: EMD-36978
TitleCryoEM map of LonC protease open hexamer with Bortezomib
Map dataCryoEM of map of LonC open hexamer with Bortezomib
Sample
  • Complex: CryoEM structure of LonC protease open hexamer with Bortezomib
    • Protein or peptide: LonC open hexamer with Bortezomib
KeywordsLon proteases / chaperone / open hexamer / inhibitor
Biological speciesMeiothermus taiwanensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36978.png

Downloads & links

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Map

FileDownload / File: emd_36978.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM of map of LonC open 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: 0.06
Minimum - Maximum-0.12510058 - 0.23480417
Average (Standard dev.)0.00083725527 (±0.012247841)
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 of map of LonC open hexamer with Bortezomib

Fileemd_36978_additional_1.map
AnnotationCryoEM of map of LonC open hexamer with Bortezomib
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM of map of LonC open hexamer with Bortezomib

Fileemd_36978_half_map_1.map
AnnotationCryoEM of map of LonC open hexamer with Bortezomib
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM of map of LonC open hexamer with Bortezomib

Fileemd_36978_half_map_2.map
AnnotationCryoEM of map of LonC open 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 open hexamer with Bortezomib

EntireName: CryoEM structure of LonC protease open hexamer with Bortezomib
Components
  • Complex: CryoEM structure of LonC protease open hexamer with Bortezomib
    • Protein or peptide: LonC open hexamer with Bortezomib

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

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

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Macromolecule #1: LonC open hexamer with Bortezomib

MacromoleculeName: LonC open hexamer with Bortezomib / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Meiothermus taiwanensis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLSYEALEW RTPIENSTEP VSLPPPPPFF GQERAREALE LAIRGGFHAY LVGPPSLGKH EALLAYLSTQ SVETPPDLLY VPLSERKVAV LTLPSGQEIH LAEAVEGLLL EVNRLDELFR QGSFLREKTQ LEARFKEARE QQLEALRREA QEAGFALSTN GERLELTGPG ...String:
MRLSYEALEW RTPIENSTEP VSLPPPPPFF GQERAREALE LAIRGGFHAY LVGPPSLGKH EALLAYLSTQ SVETPPDLLY VPLSERKVAV LTLPSGQEIH LAEAVEGLLL EVNRLDELFR QGSFLREKTQ LEARFKEARE QQLEALRREA QEAGFALSTN GERLELTGPG PVPAELSARL EEVTLGSLAA SAELEVALRR LRRDWALHYL NNRFEPLFQR FPQARAYLEA LRARLARYAE TGEPLDPAQW RPNLLTSSSS GTPPPIVYEP YATAPRLFGR LDYLVDRGVW STNVSLIRPG AVHRAQGGYL ILDALSLKRE GTWEAFKRAL RNGQVEPVTE PQAPAGLEVE PFPIQMQVIL VGTPEAFEGL EEDPAFSELF RIRAEFSPTL PASPENCTAL GGWLLAQGFQ LTQGGLTRLY DEARRMAEQR DRMDARLVEI RALAEEAAVL GGGLLTAESV EQAIAAREHR SFLSEEEFLR AVQEGVIRLR TTGRAVGEVN SLVVVEAAPY WGRPARLTAR AAPGRDHLIS IDREAGLGGQ IFHKAVLTLA GYLRSRYIEH GSLPVTISLA FEQNYVSIEG DSAGLAELVA ALSAIGNLPL RQDLAVTGAV DQTGKVLAVG AINAKVEGFF RVCKALGLSG TQGVILPEAN LANLTLRAEV LEAVRAGQFH IYAVETAEQA LEILAGARME GFRGLQEKIR AGLEAFARLE EGHDKEDREK LAAALEHHHH HH

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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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 39909
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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