[English] 日本語
Yorodumi
- EMDB-7951: cryo-EM density map of ClpP from Staphylococcus aureus with bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7951
Titlecryo-EM density map of ClpP from Staphylococcus aureus with bound Acyldepsipeptide (V7A mutant)
Map data
Sample
  • Complex: Caseinolytic protease from Staphylococcus aureus
    • Protein or peptide: Caseinolytic protease from Staphylococcus aureus
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsRipstein ZA / Vahidi S / Kay LE / Rubinstein JL
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Reversible inhibition of the ClpP protease via an N-terminal conformational switch.
Authors: Siavash Vahidi / Zev A Ripstein / Massimiliano Bonomi / Tairan Yuwen / Mark F Mabanglo / Jordan B Juravsky / Kamran Rizzolo / Algirdas Velyvis / Walid A Houry / Michele Vendruscolo / John L ...Authors: Siavash Vahidi / Zev A Ripstein / Massimiliano Bonomi / Tairan Yuwen / Mark F Mabanglo / Jordan B Juravsky / Kamran Rizzolo / Algirdas Velyvis / Walid A Houry / Michele Vendruscolo / John L Rubinstein / Lewis E Kay /
Abstract: Protein homeostasis is critically important for cell viability. Key to this process is the refolding of misfolded or aggregated proteins by molecular chaperones or, alternatively, their degradation ...Protein homeostasis is critically important for cell viability. Key to this process is the refolding of misfolded or aggregated proteins by molecular chaperones or, alternatively, their degradation by proteases. In most prokaryotes and in chloroplasts and mitochondria, protein degradation is performed by the caseinolytic protease ClpP, a tetradecamer barrel-like proteolytic complex. Dysregulating ClpP function has shown promise in fighting antibiotic resistance and as a potential therapy for acute myeloid leukemia. Here we use methyl-transverse relaxation-optimized spectroscopy (TROSY)-based NMR, cryo-EM, biochemical assays, and molecular dynamics simulations to characterize the structural dynamics of ClpP from (SaClpP) in wild-type and mutant forms in an effort to discover conformational hotspots that regulate its function. Wild-type SaClpP was found exclusively in the active extended form, with the N-terminal domains of its component protomers in predominantly β-hairpin conformations that are less well-defined than other regions of the protein. A hydrophobic site was identified that, upon mutation, leads to unfolding of the N-terminal domains, loss of SaClpP activity, and formation of a previously unobserved split-ring conformation with a pair of 20-Å-wide pores in the side of the complex. The extended form of the structure and partial activity can be restored via binding of ADEP small-molecule activators. The observed structural plasticity of the N-terminal gates is shown to be a conserved feature through studies of and ClpP, suggesting a potential avenue for the development of molecules to allosterically modulate the function of ClpP.
History
DepositionMay 29, 2018-
Header (metadata) releaseJun 27, 2018-
Map releaseJun 27, 2018-
UpdateJul 25, 2018-
Current statusJul 25, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.38
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.38
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7951.png

Downloads & links

-
Map

FileDownload / File: emd_7951.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 160 pix.
= 232. Å		1.45 Å/pix.
x 160 pix.
= 232. Å		1.45 Å/pix.
x 160 pix.
= 232. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38 / Movie #1: 0.38
Minimum - Maximum-0.58350974 - 1.3202851
Average (Standard dev.)0.005069425 (±0.07511473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 232.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z232.000232.000232.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.5841.3200.005

-
Supplemental data

-
Sample components

-
Entire : Caseinolytic protease from Staphylococcus aureus

EntireName: Caseinolytic protease from Staphylococcus aureus
Components
  • Complex: Caseinolytic protease from Staphylococcus aureus
    • Protein or peptide: Caseinolytic protease from Staphylococcus aureus

-
Supramolecule #1: Caseinolytic protease from Staphylococcus aureus

SupramoleculeName: Caseinolytic protease from Staphylococcus aureus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria) / Strain: Newman
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) CodonPlus / Recombinant plasmid: pET24
Molecular weightExperimental: 301 KDa

-
Macromolecule #1: Caseinolytic protease from Staphylococcus aureus

MacromoleculeName: Caseinolytic protease from Staphylococcus aureus / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Staphylococcus aureus (bacteria) / Strain: Newman
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLIPTAIET TNRGERAYDI YSRLLKDRII MLGSQIDDNV ANSIVSQLLF LQAQDSEKDI YLYINSPGGS VTAGFAIYDT IQHIKPDVQT ICIGMAASMG SFLLAAGAKG KRFALPNAEV MIHQPLGGAQ GQATEIEIAA NHILKTREKL NRILSERTGQ SIEKIQKDTD ...String:
MNLIPTAIET TNRGERAYDI YSRLLKDRII MLGSQIDDNV ANSIVSQLLF LQAQDSEKDI YLYINSPGGS VTAGFAIYDT IQHIKPDVQT ICIGMAASMG SFLLAAGAKG KRFALPNAEV MIHQPLGGAQ GQATEIEIAA NHILKTREKL NRILSERTGQ SIEKIQKDTD RDNFLTAEEA KEYGLIDEVM VPETK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration30 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
100.0 mMKClpotassium chloride
1.0 mMEDTAethylenediaminetetraacetic acid
5.0 mMMgCl2magnesium chloride
5.0 %Igepal CA-630
50.0 mMimidazole
GridSupport film - topology: HOLEY / Support film - Film thickness: 35.0 nm / Details: unspecified
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: Modified Vitrobot.

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 75 / Average exposure time: 15.0 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.2 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 25000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 76614
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: INSILICO MODEL / Details: Ab initio algorithm in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.5) / Number images used: 37133
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 0.5)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 0.5)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC

+
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