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- EMDB-8590: Subtomogram average of ribosome from Trypanosoma brucei -

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Basic information

Entry
Database: EMDB / ID: EMD-8590
TitleSubtomogram average of ribosome from Trypanosoma brucei
Map dataSubtomogram average of ribosome from Trypanosoma brucei
Sample
  • Complex: Ribosomes in cell
Function / homology
Function and homology information


organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / regulation of cell growth / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / regulation of cell population proliferation / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / : / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e ...Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / : / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L1, conserved site / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L44 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L30e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / : / 40S ribosomal protein S1/3, eukaryotes / 60S ribosomal protein L19 / Ribosomal Protein L6, KOW domain / Ribosomal protein L30/YlxQ / Ribosomal protein L7A/L8
Similarity search - Domain/homology
60S ribosomal protein L44 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL14 / 60S ribosomal protein L27, putative / 60S ribosomal protein L18a / 40S ribosomal protein S17, putative / Guanine nucleotide-binding protein beta subunit-like protein / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL22 ...60S ribosomal protein L44 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL14 / 60S ribosomal protein L27, putative / 60S ribosomal protein L18a / 40S ribosomal protein S17, putative / Guanine nucleotide-binding protein beta subunit-like protein / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL34 / 40S ribosomal protein S27, putative / Ribosomal protein / 40S ribosomal protein S26 / 40S ribosomal protein S21, putative / 40S ribosomal protein S5, putative / Large ribosomal subunit protein eL28 / 60S ribosomal protein L17, putative / 40S ribosomal protein S12 / 40S ribosomal protein S4 / Ribosomal protein L37 / 40S ribosomal protein S2, putative / 40S ribosomal protein S3 / 60S ribosomal protein L6, putative / 40S ribosomal protein S24 / 60S ribosomal protein L37a, putative / 60S ribosomal protein L24, putative / 40S ribosomal protein S10, putative / 40S ribosomal protein S18, putative / 60S ribosomal protein L30 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L9, putative / 40S ribosomal protein S23, putative / 40S ribosomal proteins S11, putative / 60S ribosomal protein L32, putative / 40S ribosomal protein S6 / Ribosomal protein L36, putative / Ribosomal protein L15 / 60S ribosomal protein L5, putative / 60S ribosomal protein L26, putative / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L27a / 60S ribosomal protein L23, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L11, putative / 40S ribosomal protein S7 / 60S ribosomal protein L38, putative / 60S ribosomal protein L35, putative / 60S ribosomal protein L21E, putative / 40S ribosomal protein S14 / 40S ribosomal protein S33, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L7, putative / 60S ribosomal protein L13 / 60S ribosomal protein L7a / 40S ribosomal protein S9, putative / 40S ribosomal protein S16, putative / 60S ribosomal protein L2, putative / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S15, putative / 40S ribosomal protein S25 / 60S ribosomal protein L12, putative / 40S ribosomal protein S8 / 60S ribosomal protein L23a / 60S ribosomal protein L19, putative / 40S ribosomal protein S15a, putative / Ribosomal protein L3, mitochondrial, putative / 60S ribosomal protein L4 / Ribosomal protein S19, putative / 60S ribosomal protein L35A, putative / 40S ribosomal protein S30 / 60S ribosomal protein L13a, putative / 40S ribosomal protein S13, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 38.5 Å
AuthorsChen M / Sun SY / Ludtke SJ / He CY / Schmid MF / Chiu W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139, P01NS092525, P41GM103832 United States
CitationJournal: Nat Methods / Year: 2017
Title: Convolutional neural networks for automated annotation of cellular cryo-electron tomograms.
Authors: Muyuan Chen / Wei Dai / Stella Y Sun / Darius Jonasch / Cynthia Y He / Michael F Schmid / Wah Chiu / Steven J Ludtke /
Abstract: Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components ...Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components within the crowded cellular environment. We introduce a method that uses neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yield in situ structures of molecular components of interest. The method is available in the EMAN2.2 software package.
History
DepositionFeb 3, 2017-
Header (metadata) releaseMar 1, 2017-
Map releaseMar 1, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8590.png

Downloads & links

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Map

FileDownload / File: emd_8590.map.gz / Format: CCP4 / Size: 432.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of ribosome from Trypanosoma brucei
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.6 Å/pix.
x 48 pix.
= 508.8 Å		10.6 Å/pix.
x 48 pix.
= 508.8 Å		10.6 Å/pix.
x 48 pix.
= 508.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.3324096 - 3.3328924
Average (Standard dev.)0.046224106 (±0.3001177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-24-24-24
Dimensions484848
Spacing484848
CellA=B=C: 508.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.610.610.6
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z508.800508.800508.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-24-24-24
NC/NR/NS484848
D min/max/mean-1.3323.3330.046

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Supplemental data

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Sample components

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Entire : Ribosomes in cell

EntireName: Ribosomes in cell
Components
  • Complex: Ribosomes in cell

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Supramolecule #1: Ribosomes in cell

SupramoleculeName: Ribosomes in cell / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Trypanosoma brucei (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Detector mode: INTEGRATING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 38.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.2) / Number subtomograms used: 511
ExtractionNumber tomograms: 1 / Number images used: 759 / Method: Automated tomogram segmentation / Software - Name: EMAN (ver. 2.2) / Software - details: Tomoseg tool
Final angle assignmentType: OTHER / Software - Name: EMAN (ver. 2.2) / Details: Single particle tomography tool in EMAN2

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