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- EMDB-1637: Proteome organization in a genome-reduced bacterium -Topoisomeras... -

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Basic information

Entry
Database: EMDB / ID: EMD-1637
TitleProteome organization in a genome-reduced bacterium -Topoisomerase of Mycoplasma pneumoniae -
Map dataMap of topoisomerase
Sample
  • Sample: Topoisomerase from Mycoplasma pneumoniae
  • Protein or peptide: Topoisomerase
KeywordsTopoisomerase / Mycoplasma pneumoniae / single particle
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Methodsingle particle reconstruction / negative staining / Resolution: 21.5 Å
AuthorsKuhner S / vanNoort V / Betts MJ / Leo-Macias A / Batisse C / Rode M / Yamada T / Maier T / Bader S / Beltran-Alvarez P ...Kuhner S / vanNoort V / Betts MJ / Leo-Macias A / Batisse C / Rode M / Yamada T / Maier T / Bader S / Beltran-Alvarez P / Castano-Diez D / Chen W-H / Devos D / Guell Cargol M / Norambuena T / Racke I / Rybin V / Schmidt A / Yus E / Aebersold R / Herrmann R / Bottcher B / Frangakis AS / Russell RB / Serrano L / Bork P / Gavin A-C
CitationJournal: Science / Year: 2009
Title: Proteome organization in a genome-reduced bacterium.
Authors: Sebastian Kühner / Vera van Noort / Matthew J Betts / Alejandra Leo-Macias / Claire Batisse / Michaela Rode / Takuji Yamada / Tobias Maier / Samuel Bader / Pedro Beltran-Alvarez / Daniel ...Authors: Sebastian Kühner / Vera van Noort / Matthew J Betts / Alejandra Leo-Macias / Claire Batisse / Michaela Rode / Takuji Yamada / Tobias Maier / Samuel Bader / Pedro Beltran-Alvarez / Daniel Castaño-Diez / Wei-Hua Chen / Damien Devos / Marc Güell / Tomas Norambuena / Ines Racke / Vladimir Rybin / Alexander Schmidt / Eva Yus / Ruedi Aebersold / Richard Herrmann / Bettina Böttcher / Achilleas S Frangakis / Robert B Russell / Luis Serrano / Peer Bork / Anne-Claude Gavin /
Abstract: The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification- ...The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification-mass spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the majority are novel. About a third of the heteromultimeric complexes show higher levels of proteome organization, including assembly into larger, multiprotein complex entities, suggesting sequential steps in biological processes, and extensive sharing of components, implying protein multifunctionality. Incorporation of structural models for 484 proteins, single-particle electron microscopy, and cellular electron tomograms provided supporting structural details for this proteome organization. The data set provides a blueprint of the minimal cellular machinery required for life.
History
DepositionAug 3, 2009-
Header (metadata) releaseJun 11, 2010-
Map releaseJun 11, 2010-
UpdateJun 11, 2010-
Current statusJun 11, 2010Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1637.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of topoisomerase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.2 Å/pix.
x 64 pix.
= 332.8 Å
5.2 Å/pix.
x 64 pix.
= 332.8 Å
5.2 Å/pix.
x 64 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.2 Å
Density
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum0.0 - 72.125500000000002
Average (Standard dev.)0.291584 (±2.90852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 332.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean0.00072.1250.292

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Supplemental data

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Sample components

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Entire : Topoisomerase from Mycoplasma pneumoniae

EntireName: Topoisomerase from Mycoplasma pneumoniae
Components
  • Sample: Topoisomerase from Mycoplasma pneumoniae
  • Protein or peptide: Topoisomerase

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Supramolecule #1000: Topoisomerase from Mycoplasma pneumoniae

SupramoleculeName: Topoisomerase from Mycoplasma pneumoniae / type: sample / ID: 1000 / Details: Sample was fixed following the GRAFIX protocol / Number unique components: 1

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Macromolecule #1: Topoisomerase

MacromoleculeName: Topoisomerase / type: protein_or_peptide / ID: 1 / Name.synonym: Topoisomerase / Recombinant expression: Yes
Source (natural)Organism: Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Recombinant expressionOrganism: Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)

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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

BufferpH: 7.5
Details: 50mM Hepes, 20% glycerol, 0.075% glutaraldehyde, 100mM NaCl, 1.5 mM MgCl2
StainingType: NEGATIVE
Details: Grids were prepared by sandwich negative stain the sample was adsorbed to carbon on mica and floated on 1 % uranyl acetate the carbon was picked up with an uncoated grid then a second piece ...Details: Grids were prepared by sandwich negative stain the sample was adsorbed to carbon on mica and floated on 1 % uranyl acetate the carbon was picked up with an uncoated grid then a second piece of carbon, which was also floated on 1% uranyl acetate, was picked up with the same grid sandwiching the sample between the two layers of carbon
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal magnification: 27500
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
Alignment procedureLegacy - Astigmatism: Corrected at 200000 times magnification on graininess of carbon
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 14.22 µm / Number real images: 70
Details: Images were recorded on CCD, no scanning sampling step size was adjusted to calibrated image size
Bits/pixel: 12

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, SPIDER, EMAN
Details: Spider option BP 32F Back Projection - 3D, Sampled, Interpolated in Fourier space
Number images used: 4767

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