[English] 日本語
Yorodumi
- EMDB-31607: Processive cleavage of substrate at individual proteolytic active... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31607
TitleProcessive cleavage of substrate at individual proteolytic active sites of the Lon protease complex (conformation 3)
Map data
SampleLon bound to endogenous substrate:
Lon proteaseLon protease family / Unknown endogenous substrate / (ligand) x 2
Function / homology
Function and homology information


endopeptidase La / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Lon protease, bacterial / ATP-dependent serine proteases, lon family, serine active site. / Peptidase S16, active site / Lon protease, bacterial/eukaryotic-type / Peptidase S16, Lon proteolytic domain / Lon protease (S16) C-terminal proteolytic domain / Lon protease / Lon proteolytic domain profile. / Lon N-terminal domain profile. / ATP-dependent protease La (LON) substrate-binding domain ...Lon protease, bacterial / ATP-dependent serine proteases, lon family, serine active site. / Peptidase S16, active site / Lon protease, bacterial/eukaryotic-type / Peptidase S16, Lon proteolytic domain / Lon protease (S16) C-terminal proteolytic domain / Lon protease / Lon proteolytic domain profile. / Lon N-terminal domain profile. / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Lon, substrate-binding domain / 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 speciesMeiothermus taiwanensis WR-220 (bacteria) / Meiothermus taiwanensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsLi S / Hsieh K / Kuo C / Su S / Huang K / Zhang K / Chang CI
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2320-B-001-011-MY3 Taiwan
CitationJournal: Sci Adv / Year: 2021
Title: Processive cleavage of substrate at individual proteolytic active sites of the Lon protease complex.
Authors: Shanshan Li / Kan-Yen Hsieh / Chiao-I Kuo / Shih-Chieh Su / Kai-Fa Huang / Kaiming Zhang / Chung-I Chang /
Abstract: [Figure: see text].
History
DepositionAug 1, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7fiz
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_31607.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 0.252 / Movie #1: 0.3
Minimum - Maximum-1.1226509 - 2.2209208
Average (Standard dev.)0.0009323052 (±0.09954376)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z275.520275.520275.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-1.1232.2210.001

-
Supplemental data

-
Sample components

+
Entire Lon bound to endogenous substrate

EntireName: Lon bound to endogenous substrate / Number of Components: 5

+
Component #1: protein, Lon bound to endogenous substrate

ProteinName: Lon bound to endogenous substrate / Recombinant expression: No
MassExperimental: 600 kDa
SourceSpecies: Meiothermus taiwanensis WR-220 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #2: protein, Lon protease

ProteinName: Lon proteaseLon protease family / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 90.081336 kDa
SourceSpecies: Meiothermus taiwanensis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #3: protein, Unknown endogenous substrate

ProteinName: Unknown endogenous substrate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.890321 kDa
SourceSpecies: Meiothermus taiwanensis WR-220 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: ligand, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.523247 kDa

+
Component #5: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen Name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 48 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 77159
3D reconstructionSoftware: cryoSPARC / Resolution: 3.28 Å / Resolution Method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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