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- EMDB-5290: The cryo-EM map of DegQ 12-mer -

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Basic information

Entry
Database: EMDB / ID: EMD-5290
TitleThe cryo-EM map of DegQ 12-mer
Map dataThis is a cryo-EM map of DegQ 12-mer.
Sample
  • Sample: DegQ
  • Protein or peptide: DegQ
KeywordsHtrA / 12-mer
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsBai XC / Wang XJ / Ye YY / Pan XJ / Chang LF / Leng D / Sui SF
CitationJournal: Structure / Year: 2011
Title: Characterization of the structure and function of Escherichia coli DegQ as a representative of the DegQ-like proteases of bacterial HtrA family proteins.
Authors: Xiao-chen Bai / Xi-jiang Pan / Xiao-jing Wang / Yun-ying Ye / Lei-fu Chang / Dong Leng / Jianlin Lei / Sen-Fang Sui /
Abstract: HtrA family proteins play a central role in protein quality control in the bacterial periplasmic space. DegQ-like proteases, a group of bacterial HtrA proteins, are characterized by a short LA loop ...HtrA family proteins play a central role in protein quality control in the bacterial periplasmic space. DegQ-like proteases, a group of bacterial HtrA proteins, are characterized by a short LA loop as compared with DegP-like proteases, and are found in many bacterial species. As a representative of the DegQ-like proteases, we report that Escherichia coli DegQ exists in vivo primarily as a trimer (substrate-free) or dodecamer (substrate-containing). Biochemical analysis of DegQ dodecamers revealed that the major copurified protein substrate is OmpA. Importantly, wild-type DegQ exhibited a much lower proteolytic activity, and thus higher chaperone-like activity, than DegP. Furthermore, using cryo-electron microscopy we determined high-resolution structures of DegQ 12- and 24-mers in the presence of substrate, thus revealing the structural mechanism by which DegQ moderates its proteolytic activity.
History
DepositionMay 13, 2011-
Header (metadata) releaseMay 25, 2011-
Map releaseSep 7, 2011-
UpdateSep 7, 2011-
Current statusSep 7, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5290_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5290.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cryo-EM map of DegQ 12-mer.
Voxel sizeX=Y=Z: 1.46 Å
Density
Contour LevelBy AUTHOR: 1.18 / Movie #1: 1.18
Minimum - Maximum-0.0256609 - 1.50396
Average (Standard dev.)0.163268 (±0.378047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 210.24 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.461.461.46
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z210.240210.240210.240
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-0.0261.5040.163

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Supplemental data

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Sample components

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Entire : DegQ

EntireName: DegQ
Components
  • Sample: DegQ
  • Protein or peptide: DegQ

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Supramolecule #1000: DegQ

SupramoleculeName: DegQ / type: sample / ID: 1000 / Oligomeric state: 12-mer / Number unique components: 12
Molecular weightExperimental: 500 KDa / Theoretical: 500 KDa / Method: size-exclusion chromatography

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Macromolecule #1: DegQ

MacromoleculeName: DegQ / type: protein_or_peptide / ID: 1 / Name.synonym: DegQ / Number of copies: 12 / Oligomeric state: 12-mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: Escherichia coli / Location in cell: periplasmic
Molecular weightExperimental: 45 MDa / Theoretical: 45 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET-28a

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.6 / Details: 40 mM Na2HPO4, 10 mM NaH2PO4, 25 mM NaCl
GridDetails: 400 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Vitrification instrument: Vitrobot Mark IV / Method: Blot for 1.5 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 102740 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
DateJan 3, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 15 µm / Number real images: 315 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final two d classificationNumber classes: 180
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 24604

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