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- EMDB-1913: Structure of the Listeria monocytogenes ClpP1P2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-1913
TitleStructure of the Listeria monocytogenes ClpP1P2 complex
Map dataThis is a surface rendered side view of ClpP1P2
Sample
  • Sample: Listeria monocytogenes ClpP1P2 complex
  • Protein or peptide: ClpP1
  • Protein or peptide: ClpP2
KeywordsProteomics / Vibralactone / heat shock protein / peptidase ClpP
Biological speciesListeria monocytogenes (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsZeiler E / Braun N / Boettcher T / Kastenmueller A / Weinkauf S / Sieber S
CitationJournal: Angew Chem Int Ed Engl / Year: 2011
Title: Vibralactone as a tool to study the activity and structure of the ClpP1P2 complex from Listeria monocytogenes.
Authors: Evelyn Zeiler / Nathalie Braun / Thomas Böttcher / Andreas Kastenmüller / Sevil Weinkauf / Stephan A Sieber /
History
DepositionJun 23, 2011-
Header (metadata) releaseJul 8, 2011-
Map releaseNov 25, 2011-
UpdateNov 25, 2011-
Current statusNov 25, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1913.jpg

Downloads & links

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Map

FileDownload / File: emd_1913.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a surface rendered side view of ClpP1P2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 128 pix.
= 186.88 Å		1.46 Å/pix.
x 128 pix.
= 186.88 Å		1.46 Å/pix.
x 128 pix.
= 186.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.230148 - 0.236633
Average (Standard dev.)0.00652331 (±0.0323232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 186.88 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.461.461.46
M x/y/z128128128
origin x/y/z-0.000-0.000-0.000
length x/y/z186.880186.880186.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.2300.2370.007

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Supplemental data

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Sample components

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Entire : Listeria monocytogenes ClpP1P2 complex

EntireName: Listeria monocytogenes ClpP1P2 complex
Components
  • Sample: Listeria monocytogenes ClpP1P2 complex
  • Protein or peptide: ClpP1
  • Protein or peptide: ClpP2

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Supramolecule #1000: Listeria monocytogenes ClpP1P2 complex

SupramoleculeName: Listeria monocytogenes ClpP1P2 complex / type: sample / ID: 1000 / Oligomeric state: Tetradecamer / Number unique components: 2
Molecular weightExperimental: 310 KDa / Theoretical: 310 KDa

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Macromolecule #1: ClpP1

MacromoleculeName: ClpP1 / type: protein_or_peptide / ID: 1 / Name.synonym: ClpP1 / Number of copies: 1 / Oligomeric state: Heptamer / Recombinant expression: Yes
Source (natural)Organism: Listeria monocytogenes (bacteria)

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Macromolecule #2: ClpP2

MacromoleculeName: ClpP2 / type: protein_or_peptide / ID: 2 / Name.synonym: ClpP2 / Number of copies: 1 / Oligomeric state: Heptamer / Recombinant expression: Yes
Source (natural)Organism: Listeria monocytogenes (bacteria)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7 / Details: 50 mM MES, 100 mM KCl, 5% glycerol
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 1.5% w/v uranyl acetate for 30 seconds.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 100CX
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Image recordingDigitization - Scanner: OTHER / Number real images: 16 / Bits/pixel: 16
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 58000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.8 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: eucentric / Specimen holder model: JEOL

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Image processing

CTF correctionDetails: Phase flipping
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Number images used: 39116
Final two d classificationNumber classes: 64

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