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- EMDB-3735: Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-... -

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Basic information

Entry
Database: EMDB / ID: 3735
TitleClass 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown
SampleClass 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataClass 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown
Methodsingle particle reconstruction, at 7 Å resolution
AuthorsMatsuo Y / Ikeuchi K / Saeki Y / Iwasaki S / Schmidt C / Udagawa T / Sato F / Tsuchiya H / Becker T / Tanaka K / Ingolia N / Beckmann R / Inada T
CitationNat Commun, 2017, 8, 159-159

Nat Commun, 2017, 8, 159-159 StrPapers
Ubiquitination of stalled ribosome triggers ribosome-associated quality control.
Yoshitaka Matsuo / Ken Ikeuchi / Yasushi Saeki / Shintaro Iwasaki / Christian Schmidt / Tsuyoshi Udagawa / Fumiya Sato / Hikaru Tsuchiya / Thomas Becker / Keiji Tanaka / Nicholas T Ingolia / Roland Beckmann / Toshifumi Inada

DateDeposition: May 23, 2017 / Header (metadata) release: May 31, 2017 / Map release: Aug 9, 2017 / Last update: Aug 9, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.027
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3735.map.gz (map file in CCP4 format, 8789 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
3.25 Å/pix.
= 422.76 Å
130 pix
3.25 Å/pix.
= 422.76 Å
130 pix
3.25 Å/pix.
= 422.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.252 Å
Density
Contour Level:0.027 (by author), 0.027 (movie #1):
Minimum - Maximum-0.07632151 - 0.23760337
Average (Standard dev.)-0.0006627558 (0.02365276)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin000
Limit129129129
Spacing130130130
CellA=B=C: 422.76 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.2523.2523.252
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z422.760422.760422.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-0.0760.238-0.001

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Supplemental data

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Sample components

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Entire Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-...

EntireName: Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown
Details: Third class from classification for dataset in Frealign
Number of components: 1
MassTheoretical: 3.6 MDa

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Component #1: protein, Class 2 of rotated ribosomes (rotated 1 state) with A/A-...

ProteinName: Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown
Details: Third class from classification for dataset in Frealign
Recombinant expression: No
MassTheoretical: 3.6 MDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 28 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 31858
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF

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