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- EMDB-10009: Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles (State... -

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Basic information

Entry
Database: EMDB / ID: EMD-10009
TitleCryo-EM structures of Lsg1-TAP pre-60S ribosomal particles (State III - subclass 1)
Map data
Sample
  • Complex: Lsg1-TAP 60s ribosomal subunit
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKargas V / Warren AJ
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Bloodwise12048 United Kingdom
Medical Research Council (United Kingdom)105161083 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Authors: Kargas V / Warren AJ
History
DepositionMay 31, 2019-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10009.png

Downloads & links

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Map

FileDownload / File: emd_10009.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.021652829 - 0.09056228
Average (Standard dev.)0.0016960776 (±0.0076064067)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 383.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z383.400383.400383.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0220.0910.002

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Supplemental data

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Sample components

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Entire : Lsg1-TAP 60s ribosomal subunit

EntireName: Lsg1-TAP 60s ribosomal subunit
Components
  • Complex: Lsg1-TAP 60s ribosomal subunit

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Supramolecule #1: Lsg1-TAP 60s ribosomal subunit

SupramoleculeName: Lsg1-TAP 60s ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#48
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 63.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: Gctf (ver. 1.06), CTFFIND (ver. 4.1))
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 27769

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Atomic model buiding 1

Initial modelPDB ID:

4v88

RefinementProtocol: FLEXIBLE FIT

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