[English] 日本語
Yorodumi
- EMDB-13232: Lon protease from Thermus Thermophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13232
TitleLon protease from Thermus ThermophilusLon protease family
Map data
Sample
  • Complex: Lon protease from Thermus thermophilusLon protease family
    • Protein or peptide: Lon proteaseLon protease family
    • Protein or peptide: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Lon protease, bacterial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon N-terminal domain profile. / Lon protease, N-terminal domain ...Lon protease, bacterial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCoscia F / Lowe J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
Wellcome Trust202754/Z/16/Z United Kingdom
CitationJournal: FEBS Lett / Year: 2021
Title: Cryo-EM structure of the full-length Lon protease from Thermus thermophilus.
Authors: Francesca Coscia / Jan Löwe /
Abstract: In bacteria, Lon is a large hexameric ATP-dependent protease that targets misfolded and also folded substrates, some of which are involved in cell division and survival of cellular stress. The N- ...In bacteria, Lon is a large hexameric ATP-dependent protease that targets misfolded and also folded substrates, some of which are involved in cell division and survival of cellular stress. The N-terminal domain of Lon facilitates substrate recognition, but how the domains confer such activity has remained unclear. Here, we report the full-length structure of Lon protease from Thermus thermophilus at 3.9 Å resolution in a substrate-engaged state. The six N-terminal domains are arranged in three pairs, stabilized by coiled-coil segments and forming an additional channel for substrate sensing and entry into the AAA+ ring. Sequence conservation analysis and proteolysis assays confirm that this architecture is required for the degradation of both folded and unfolded substrates in bacteria.
History
DepositionJul 18, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7p6u
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7p6u
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13232.png

Downloads & links

-
Map

FileDownload / File: emd_13232.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0166 / Movie #1: 0.014
Minimum - Maximum-0.035448316 - 0.07020605
Average (Standard dev.)0.00031472597 (±0.002590182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0350.0700.000

-
Supplemental data

-
Additional map: #1

Fileemd_13232_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Lon protease from Thermus thermophilus

EntireName: Lon protease from Thermus thermophilusLon protease family
Components
  • Complex: Lon protease from Thermus thermophilusLon protease family
    • Protein or peptide: Lon proteaseLon protease family
    • Protein or peptide: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

-
Supramolecule #1: Lon protease from Thermus thermophilus

SupramoleculeName: Lon protease from Thermus thermophilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Engaged with a peptide substrate, nucleotide AMP-PNP
Source (natural)Organism: Thermus thermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

-
Macromolecule #1: Lon protease

MacromoleculeName: Lon protease / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: endopeptidase La
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 89.442945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKDFLRLELP VLPLRNTVVL PHTTTGVDVG RLKSKRAVEE ALSADRLLFL VTQKDPEVDD PAPEDLYAVG TLAVVKQAMR LPDGTLQVM VEARSRARLL SYVAAPYLRA VGEAIPEPPL KDPELARVLV NEVQEAFERY LQNHKTLRLD RYQQEAVKST R DPAILADL ...String:
MKDFLRLELP VLPLRNTVVL PHTTTGVDVG RLKSKRAVEE ALSADRLLFL VTQKDPEVDD PAPEDLYAVG TLAVVKQAMR LPDGTLQVM VEARSRARLL SYVAAPYLRA VGEAIPEPPL KDPELARVLV NEVQEAFERY LQNHKTLRLD RYQQEAVKST R DPAILADL VAHHATWTLE EKQTILETPE VEERLKRVLA LLLRDLERFE LDKKIAARVK EQMDQNQREY YLREQMKAIQ KE LGGGEDF LTEIEELRER IEKKGMPEPV KEKALKELKR LERMQPGSPE ATVSRTYLDW LLEVPWTEAD PEVLDISVTK RVL DEDHYG LKEVKERILE YLAVRQLTQG KEVKGHAPIL CFVGPPGVGK TSLGKSIARS MNRRFHRISL GGVRDEAEIR GHRR TYIGA LPGKIIQGMK QVGVVNPVFL LDEIDKLSSD WRGDPAAALL EVLDPEQNHT FTDHYLDVPY DLSKVFFITT ANTLS TIPR PLLDRMEVIE IPGYTLHEKR AIARYFRWPF QVKEAGLEGR LEITDRAIER IVQEYTREAG VRNLDRELSK VARKAA KDY LEKPWEGVRV VDAEDLEAYL GVPKYRPDRA EKEPQVGAAQ GLAWTPYGGT LLTIEAVAVP GTGKVNLTGN LGEVMKE SA HAALTYLRAH REEWGLPEGF HKDYDLHIHV PEGATPKDGP SAGITIATAL ASALTGRPVR MDIAMTGEIT LRGRVLPI G GVKEKLLAAH QAGIHRVILP KENAAELKEV PEEILKDLEI HFVEEVGEVL KLLLLPPPPP PAVQPDRPQP GVGA

-
Macromolecule #2: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

MacromoleculeName: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) / type: protein_or_peptide / ID: 2
Details: Substrate trapped in the Lon protease chamber: it was impossible to define the sequence from the side chains density, therefore it was indicated as a poly-UNK chain
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 613.749 Da
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

-
Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 5 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6on2


Details: 6ON2 and 3LJC were used as starting models for the C-terminal (AAA+, protease) and N-terminal domains (substrate recognition)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44449
FSC plot (resolution estimation)

+
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