[English] 日本語
Yorodumi
- EMDB-1983: Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1983
TitleSymmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide
Map dataSymmetrized reconstruction of Escherichia coli DegQ 12-mer in complex with a binding peptide
Sample
  • Sample: Escherichia coli DegQ 12-mer in complex with a binding peptide
  • Protein or peptide: DegQ
  • Ligand: peptide
KeywordsChaperone / Protease
Function / homology
Function and homology information


peptidase Do / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Periplasmic pH-dependent serine endoprotease DegQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsMalet H / Canellas F / Sawa J / Yan J / Thalassinos K / Ehrmann M / Clausen T / Saibil HR
CitationJournal: Nat Struct Mol Biol / Year: 2012
Title: Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ.
Authors: Hélène Malet / Flavia Canellas / Justyna Sawa / Jun Yan / Konstantinos Thalassinos / Michael Ehrmann / Tim Clausen / Helen R Saibil /
Abstract: The HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA ...The HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA proteins are well characterized, their chaperone activity remains poorly understood. Here we describe cryo-EM structures of Escherichia coli DegQ in its 12- and 24-mer states in complex with model substrates, providing a structural model of HtrA chaperone action. Up to six lysozyme substrates bind inside the DegQ 12-mer cage and are visualized in a close-to-native state. An asymmetric reconstruction reveals the binding of a well-ordered lysozyme to four DegQ protomers. DegQ PDZ domains are located adjacent to substrate density and their presence is required for chaperone activity. The substrate-interacting regions appear conserved in 12- and 24-mer cages, suggesting a common mechanism of chaperone function.
History
DepositionNov 8, 2011-
Header (metadata) releaseDec 21, 2011-
Map releaseDec 21, 2011-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4a8c
  • Surface level: 1.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1983.png

Downloads & links

-
Map

FileDownload / File: emd_1983.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetrized reconstruction of Escherichia coli DegQ 12-mer in complex with a binding peptide
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 256 pix.
= 358.4 Å		1.4 Å/pix.
x 256 pix.
= 358.4 Å		1.4 Å/pix.
x 256 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7 / Movie #1: 1.7
Minimum - Maximum-19.514199999999999 - 49.311900000000001
Average (Standard dev.)-0.00000639604 (±1.0071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 358.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-19.51449.312-0.000

-
Supplemental data

-
Sample components

-
Entire : Escherichia coli DegQ 12-mer in complex with a binding peptide

EntireName: Escherichia coli DegQ 12-mer in complex with a binding peptide
Components
  • Sample: Escherichia coli DegQ 12-mer in complex with a binding peptide
  • Protein or peptide: DegQ
  • Ligand: peptide

-
Supramolecule #1000: Escherichia coli DegQ 12-mer in complex with a binding peptide

SupramoleculeName: Escherichia coli DegQ 12-mer in complex with a binding peptide
type: sample / ID: 1000 / Details: - / Oligomeric state: Peptide monomer bound to one DegQ 12-mer / Number unique components: 2
Molecular weightExperimental: 540 KDa / Theoretical: 540 KDa / Method: Size exclusion chromatography

-
Macromolecule #1: DegQ

MacromoleculeName: DegQ / type: protein_or_peptide / ID: 1 / Name.synonym: DegQ / Number of copies: 12 / Oligomeric state: Dodecamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12 / Location in cell: Periplasm
Molecular weightExperimental: 45 KDa / Theoretical: 45 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET26b

-
Macromolecule #2: peptide

MacromoleculeName: peptide / type: ligand / ID: 2 / Name.synonym: peptide / Details: Peptide sequence SPMFKGVLDMMYGGMRGYQV / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)
Molecular weightExperimental: 2.2 KDa / Theoretical: 2.2 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES/NaOH, 150 mM NaCl.
GridDetails: C-flat grids (CF-2/2-4C-100 Protochips)
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual plunger / Method: Blot for 2 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 92 K / Average: 91 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
Legacy - Electron beam tilt params: 0
DetailsLow dose mode
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 110 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Single tilt cryo / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Phase flipping, full CTF correction
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-5, SPIDER / Number images used: 29432

-
Atomic model buiding 1

Initial modelPDB ID:

3stj


Chain - Chain ID: A
SoftwareName: Chimera, Flex-EM
DetailsPDBEntryID_givenInChain. Protocol: Rigid body and flexible fitting. Protease and PDZ1 trimers extracted from PDB entry 3STJ.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation, energy
Output model

PDB-4a8c:
Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide

-
Atomic model buiding 2

Initial modelPDB ID:

3stj


Chain - Chain ID: B
SoftwareName: Chimera, Flex-EM
DetailsPDBEntryID_givenInChain. Protocol: Rigid body and flexible fitting. Protease and PDZ1 trimers extracted from pdb entry 3STJ.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation, energy
Output model

PDB-4a8c:
Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide

-
Atomic model buiding 3

Initial modelPDB ID:

3stj


Chain - Chain ID: C
SoftwareName: Chimera, Flex-EM
DetailsPDBEntryID_givenInChain. Protocol: Rigid body and flexible fitting. Protease and PDZ1 trimers extracted from pdb entry 3STJ.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation, energy
Output model

PDB-4a8c:
Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide

-
Atomic model buiding 4

Initial modelPDB ID:

3cs0


Chain - Chain ID: A
SoftwareName: MODELLER, Chimera, Flex-EM
DetailsPDBEntryID_givenInChain. Protocol: Rigid body and flexible fitting. PDZ2 domain (residues 377-466) modelled with MODELLER from E. coli DegP pdb entry 3CS0.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation, energy
Output model

PDB-4a8c:
Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide

+
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