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- EMDB-5805: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-F... -

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Basic information

Entry
Database: EMDB / ID: EMD-5805
TitleCryo-EM map of the Drosophila 80S Ribosome (control map for 80S-FMRP Complex map)
Map dataCryo-EM reconstruction of Drosophila 80S ribosome
Sample
  • Sample: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-FMRP Complex map)
  • Complex: 80S ribosome
KeywordsDrosophila 80S FMRP
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.2 Å
AuthorsChen E / Sharma M R / Shi X / Agrawal R K / Joseph S
CitationJournal: Mol Cell / Year: 2014
Title: Fragile X mental retardation protein regulates translation by binding directly to the ribosome.
Authors: Eileen Chen / Manjuli R Sharma / Xinying Shi / Rajendra K Agrawal / Simpson Joseph /
Abstract: Fragile X syndrome (FXS) is the most common form of inherited mental retardation, and it is caused by loss of function of the fragile X mental retardation protein (FMRP). FMRP is an RNA-binding ...Fragile X syndrome (FXS) is the most common form of inherited mental retardation, and it is caused by loss of function of the fragile X mental retardation protein (FMRP). FMRP is an RNA-binding protein that is involved in the translational regulation of several neuronal mRNAs. However, the precise mechanism of translational inhibition by FMRP is unknown. Here, we show that FMRP inhibits translation by binding directly to the L5 protein on the 80S ribosome. Furthermore, cryoelectron microscopic reconstruction of the 80S ribosome⋅FMRP complex shows that FMRP binds within the intersubunit space of the ribosome such that it would preclude the binding of tRNA and translation elongation factors on the ribosome. These findings suggest that FMRP inhibits translation by blocking the essential components of the translational machinery from binding to the ribosome.
History
DepositionNov 28, 2013-
Header (metadata) releaseJul 30, 2014-
Map releaseJul 30, 2014-
UpdateJul 30, 2014-
Current statusJul 30, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5805.gif

Downloads & links

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Map

FileDownload / File: emd_5805.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of Drosophila 80S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.78 Å/pix.
x 130 pix.
= 361.4 Å		2.78 Å/pix.
x 130 pix.
= 361.4 Å		2.78 Å/pix.
x 130 pix.
= 361.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 35.0 / Movie #1: 35
Minimum - Maximum-216.565719599999994 - 431.13583374000001
Average (Standard dev.)7.88158989 (±44.14071655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 361.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.782.782.78
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z361.400361.400361.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-216.566431.1367.882

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Supplemental data

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Sample components

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Entire : Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-F...

EntireName: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-FMRP Complex map)
Components
  • Sample: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-FMRP Complex map)
  • Complex: 80S ribosome

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Supramolecule #1000: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-F...

SupramoleculeName: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-FMRP Complex map)
type: sample / ID: 1000 / Details: monodisperse / Number unique components: 1

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: fruit fly / Tissue: embryo / Location in cell: cytoplasm
Molecular weightExperimental: 3 MDa / Theoretical: 3 MDa

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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

Concentration0.12 mg/mL
BufferpH: 7.7
Details: 50 mM KOAc, 50 mM Tris acetate, pH 7.7, 10 mM DTT, 5 mM Mg(OAc)2
GridDetails: 300 mesh Quantifoil with thin carbon support, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II / Method: Blot for 6 seconds before plunging.

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Electron microscopy

MicroscopeFEI TECNAI 20
TemperatureAverage: 120 K
DateDec 27, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 102 / Average electron dose: 10 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50760 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: liquid nitrogen-cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected using automatic selection and manual screening in SPIDER
CTF correctionDetails: each defocus volume
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.2 Å / Resolution method: OTHER / Software - Name: Spider
Details: CTF corrected volume was enhanced for high spatial frequencies.
Number images used: 78267
Final angle assignmentDetails: SPIDER:theta 15 degrees, phi 15 degrees
Final two d classificationNumber classes: 83

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