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- EMDB-10773: Structure of a human 48S translational initiation complex - eIF3bgi -

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Basic information

Entry
Database: EMDB / ID: EMD-10773
TitleStructure of a human 48S translational initiation complex - eIF3bgi
Map data
SampleEukaryotic translation initiation factor
  • (Eukaryotic translation initiation factor 3 subunit ...) x 3
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / cytoplasmic translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / cytoplasmic translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / regulation of translational initiation / translation initiation factor binding / molecular adaptor activity / translation initiation factor activity / translational initiation / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / microtubule / postsynaptic density / mRNA binding / synapse / nucleolus / structural molecule activity / RNA binding / extracellular exosome / membrane / nucleoplasm / cytosol / cytoplasm
Nucleotide-binding alpha-beta plait domain superfamily / Eukaryotic translation initiation factor 3 subunit B / WD40-repeat-containing domain superfamily / RNA-binding domain superfamily / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A / WD40 repeat, conserved site / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily ...Nucleotide-binding alpha-beta plait domain superfamily / Eukaryotic translation initiation factor 3 subunit B / WD40-repeat-containing domain superfamily / RNA-binding domain superfamily / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A / WD40 repeat, conserved site / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / RNA recognition motif domain / Translation initiation factor, beta propellor-like domain / Proteasome component (PCI) domain / WD40 repeat
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsBrito Querido J / Sokabe M / Kraatz S / Gordiyenko Y / Skehel M / Fraser C / Ramakrishnan V
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
Validation ReportPDB-ID: 6ybt

SummaryFull reportAbout validation report
History
DepositionMar 17, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ybt
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ybt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10773.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 500 pix.
= 537. Å
1.07 Å/pix.
x 500 pix.
= 537. Å
1.07 Å/pix.
x 500 pix.
= 537. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.06345737 - 0.15704522
Average (Standard dev.)0.00019368101 (±0.0034452998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 537.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z537.000537.000537.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0630.1570.000

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Supplemental data

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Segmentation: #1

Fileemd_10773_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_10773_additional.map
Projections & Slices
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Half map: #2

Fileemd_10773_half_map_1.map
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Half map: #1

Fileemd_10773_half_map_2.map
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Sample components

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Entire Eukaryotic translation initiation factor

EntireName: Eukaryotic translation initiation factor / Number of components: 4

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Component #1: protein, Eukaryotic translation initiation factor

ProteinName: Eukaryotic translation initiation factor / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Eukaryotic translation initiation factor 3 subunit A

ProteinName: Eukaryotic translation initiation factor 3 subunit A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 163.179531 kDa
SourceSpecies: Human (human)

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Component #3: protein, Eukaryotic translation initiation factor 3 subunit I

ProteinName: Eukaryotic translation initiation factor 3 subunit I / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.543773 kDa
SourceSpecies: Human (human)

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Component #4: protein, Eukaryotic translation initiation factor 3 subunit B

ProteinName: Eukaryotic translation initiation factor 3 subunit B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 92.593414 kDa
SourceSpecies: Human (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 107 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 144882
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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