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- EMDB-4331: Structure of a partial yeast 48S preinitiation complex with eIF5 ... -

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Basic information

Entry
Database: EMDB / ID: 4331
TitleStructure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (Map B)
Map dataFor optimal visualization of all tRNA, eIF2 gamma and eIF3b and eIF3i beta propellers, gauss-filter the map by 1.2 and display it at 0.02 contour level.
SampleStructure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model B):
SourceKluyveromyces lactis (yeast)
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsLlacer JL / Hussain T / Gordiyenko Y / Ramakrishnan V
CitationJournal: Elife / Year: 2018
Title: Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.
Authors: José Luis Llácer / Tanweer Hussain / Adesh K Saini / Jagpreet Singh Nanda / Sukhvir Kaur / Yuliya Gordiyenko / Rakesh Kumar / Alan G Hinnebusch / Jon R Lorsch / V Ramakrishnan
DateDeposition: Mar 12, 2018 / Header (metadata) release: Aug 24, 2016 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4331.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.34 Å/pix.
= 402. Å
300 pix
1.34 Å/pix.
= 402. Å
300 pix
1.34 Å/pix.
= 402. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.12 (by author), 0.12 (movie #1):
Minimum - Maximum-0.23156458 - 0.48808563
Average (Standard dev.)0.0000028441173 (0.020816991)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 402.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z402.000402.000402.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2320.4880.000

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Supplemental data

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Sample components

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Entire Structure of a partial yeast 48S preinitiation complex with eIF5 ...

EntireName: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model B)
Number of components: 1

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Component #1: protein, Structure of a partial yeast 48S preinitiation complex w...

ProteinName: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model B)
Recombinant expression: No
MassTheoretical: 1.8 MDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/ml / pH: 6.5
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000.0 X (nominal), 104478.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm
Specimen HolderModel: OTHER / Temperature: K ( 90.0 - 100.0 K)
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3600
Details: Images were collected in movie-mode at 32 frames per second

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 54699 / Details: FEI Falcon III
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: FSC / Refinement space: RECIPROCAL / Overall bvalue: 54

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