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- EMDB-1728: 70S Ribosome and Human U4U6U5 tri-snRNP Determined by Cryo-Random... -

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Basic information

Entry
Database: EMDB / ID: EMD-1728
Title70S Ribosome and Human U4U6U5 tri-snRNP Determined by Cryo-Random Conical Tilt
Map dataThis 3D map is a weighted average cryo RCT structure of the 70S ribosome.
Sample
  • Sample: E. coli 70S ribosome
  • Complex: Ribosome
KeywordsRibosome wRCT cryo-RCT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 31.0 Å
AuthorsSander B / Golas MM / Luhrmann R / Stark H
CitationJournal: Structure / Year: 2010
Title: An approach for de novo structure determination of dynamic molecular assemblies by electron cryomicroscopy.
Authors: Bjoern Sander / Monika M Golas / Reinhard Lührmann / Holger Stark /
Abstract: Single-particle electron cryomicroscopy is a powerful method for three-dimensional (3D) structure determination of macromolecular assemblies. Here we address the challenge of determining a 3D ...Single-particle electron cryomicroscopy is a powerful method for three-dimensional (3D) structure determination of macromolecular assemblies. Here we address the challenge of determining a 3D structure in the absence of reference models. The 3D structures are determined by alignment and weighted averaging of densities obtained by native cryo random conical tilt (RCT) reconstructions including consideration of missing data. Our weighted averaging scheme (wRCT) offers advantages for potentially heterogeneous 3D densities of low signal-to-noise ratios. Sets of aligned RCT structures can also be analyzed by multivariate statistical analysis (MSA) to provide insights into snapshots of the assemblies. The approach is used to compute 3D structures of the Escherichia coli 70S ribosome and the human U4/U6.U5 tri-snRNP under vitrified unstained cryo conditions, and to visualize by 3D MSA the L7/L12 stalk of the 70S ribosome and states of tri-snRNP. The approach thus combines de novo 3D structure determination with an analysis of compositional and conformational heterogeneity.
History
DepositionMay 10, 2010-
Header (metadata) releaseJun 11, 2010-
Map releaseJun 16, 2010-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1728.gif

1728.tif

Downloads & links

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Map

FileDownload / File: emd_1728.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis 3D map is a weighted average cryo RCT structure of the 70S ribosome.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.9 Å/pix.
x 96 pix.
= 470.4 Å		4.9 Å/pix.
x 96 pix.
= 470.4 Å		4.9 Å/pix.
x 96 pix.
= 470.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.130611 - 0.153184
Average (Standard dev.)0.000358288 (±0.0104324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions969696
Spacing969696
CellA=B=C: 470.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.94.94.9
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z470.400470.400470.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS969696
D min/max/mean-0.1310.1530.000

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Supplemental data

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Sample components

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Entire : E. coli 70S ribosome

EntireName: E. coli 70S ribosome
Components
  • Sample: E. coli 70S ribosome
  • Complex: Ribosome

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Supramolecule #1000: E. coli 70S ribosome

SupramoleculeName: E. coli 70S ribosome / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 1

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Supramolecule #1: Ribosome

SupramoleculeName: Ribosome / type: complex / ID: 1 / Name.synonym: E. coli 70S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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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

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: OTHER

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Atomic model buiding 1

Initial modelPDB ID:

2aw7
PDB Unreleased entry

DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

2awb
PDB Unreleased entry

DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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