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- EMDB-36974: CryoEM structure of LonC protease S582A open pentamer with lysozyme -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36974
TitleCryoEM structure of LonC protease S582A open pentamer with lysozyme
Map dataCryoEM map of LonC S582A open pentamer with lysozyme
Sample
  • Complex: CryoEM structure of LonC protease S582A open pentamer with lysozyme, AGS
    • Protein or peptide: Endopeptidase La
  • Ligand: Monothiophosphate
KeywordsLon proteases / chaperone / open pentamer / lysozyme
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: 3.4 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_36974.png

Downloads & links

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Map

FileDownload / File: emd_36974.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of LonC S582A open pentamer with lysozyme
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-0.5300903 - 0.8892305
Average (Standard dev.)0.0043644467 (±0.030031098)
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 S582A open pentamer with lysozyme

Fileemd_36974_additional_1.map
AnnotationCryoEM map of LonC S582A open pentamer with lysozyme
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM map of LonC S582A open pentamer with lysozyme

Fileemd_36974_half_map_1.map
AnnotationCryoEM map of LonC S582A open pentamer with lysozyme
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM map of LonC S582A open pentamer with lysozyme

Fileemd_36974_half_map_2.map
AnnotationCryoEM map of LonC S582A open pentamer with lysozyme
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 S582A open pentamer with lysozy...

EntireName: CryoEM structure of LonC protease S582A open pentamer with lysozyme, AGS
Components
  • Complex: CryoEM structure of LonC protease S582A open pentamer with lysozyme, AGS
    • Protein or peptide: Endopeptidase La
  • Ligand: Monothiophosphate

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Supramolecule #1: CryoEM structure of LonC protease S582A open pentamer with lysozy...

SupramoleculeName: CryoEM structure of LonC protease S582A open pentamer with lysozyme, AGS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Meiothermus taiwanensis (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Endopeptidase La

MacromoleculeName: Endopeptidase La / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: endopeptidase La
Source (natural)Organism: Meiothermus taiwanensis (bacteria)
Molecular weightTheoretical: 80.542352 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 NYVSIEGDAA 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: Monothiophosphate

MacromoleculeName: Monothiophosphate / type: ligand / ID: 2 / Number of copies: 3 / Formula: TS6
Molecular weightTheoretical: 114.061 Da
Chemical component information

ChemComp-TS6:
Monothiophosphate

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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: 951053
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 76024
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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