[English] 日本語
Yorodumi
- EMDB-36974: CryoEM structure of LonC protease S582A open pentamer with lysozyme -

+
Open data


ID or keywords:

Loading...

-
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-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36974.png

Downloads & links

-
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 °

-
Supplemental data

-
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)

-
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)

-
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)

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

Particle selectionNumber selected: 951053
CTF correctionType: NONE
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more