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- EMDB-10774: Structure of a human 48S translational initiation complex - eIF2-TC -

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Basic information

Entry
Database: EMDB / ID: EMD-10774
TitleStructure of a human 48S translational initiation complex - eIF2-TC
Map data
Sample48S initiation complex
  • (Eukaryotic translation initiation factor 2 subunit ...) x 3
  • (nucleic-acidNucleic acid) x 2
Function / homology
Function and homology information


male germ cell proliferation / translation initiation ternary complex / glial limiting end-foot / positive regulation of type B pancreatic cell apoptotic process / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex / translation factor activity, RNA binding ...male germ cell proliferation / translation initiation ternary complex / glial limiting end-foot / positive regulation of type B pancreatic cell apoptotic process / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex / translation factor activity, RNA binding / negative regulation of guanyl-nucleotide exchange factor activity / PERK-mediated unfolded protein response / protein-synthesizing GTPase / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / stress granule assembly / polysome / translation initiation factor binding / cellular response to amino acid starvation / response to endoplasmic reticulum stress / translation initiation factor activity / translational initiation / positive regulation of translational fidelity / cellular response to UV / cytoplasmic stress granule / positive regulation of neuron death / male gonad development / ribosome binding / cellular response to heat / cellular response to oxidative stress / transmembrane transport / in utero embryonic development / aging / cadherin binding / GTPase activity / protein autophosphorylation / mRNA binding / synapse / GTP binding / RNA binding / extracellular exosome / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Translation initiation factor 2, alpha subunit / RNA-binding domain, S1 / Translation protein, beta-barrel domain superfamily / Translation elongation factor EFTu-like, domain 2 / Translation initiation factor 2, gamma subunit, C-terminal / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor 2, alpha subunit, middle domain superfamily / Nucleic acid-binding, OB-fold / S1 domain ...Translation initiation factor 2, alpha subunit / RNA-binding domain, S1 / Translation protein, beta-barrel domain superfamily / Translation elongation factor EFTu-like, domain 2 / Translation initiation factor 2, gamma subunit, C-terminal / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor 2, alpha subunit, middle domain superfamily / Nucleic acid-binding, OB-fold / S1 domain / Translation initiation factor 2, alpha subunit, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Translation initiation factor IF2/IF5 / Transcription factor, GTP-binding domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal
Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit 3
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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: 6ybv

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: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ybv
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ybv
  • 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_10774.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: 0.025 / Movie #1: 0.035
Minimum - Maximum-0.13308457 - 0.23474605
Average (Standard dev.)0.00015950525 (±0.0037637458)
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-0.1330.2350.000

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Supplemental data

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Segmentation: #1

Fileemd_10774_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_10774_additional.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #1

Fileemd_10774_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_10774_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire 48S initiation complex

EntireName: 48S initiation complex / Number of components: 6

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Component #1: protein, 48S initiation complex

ProteinName: 48S initiation complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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

ProteinName: Eukaryotic translation initiation factor 2 subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.454484 kDa
SourceSpecies: Human (human)

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Component #3: protein, Eukaryotic translation initiation factor 2 subunit 1

ProteinName: Eukaryotic translation initiation factor 2 subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.16118 kDa
SourceSpecies: Human (human)

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Component #4: nucleic-acid, Initiator methionine tRNA

nucleic acidName: Initiator methionine tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGCAGAGUGG CGCAGCGGAA GCGUGCUGGG CCCAUAACCC AGAGGUCGAU GGAUCGAAAC CAUCCUCUGC UACCA
MassTheoretical: 24.23151 kDa
SourceSpecies: Homo sapiens (human)

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Component #5: nucleic-acid, mRNA

nucleic acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAA
MassTheoretical: 0.94266 kDa
SourceSpecies: Homo sapiens (human)

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Component #6: protein, Eukaryotic translation initiation factor 2 subunit 3

ProteinName: Eukaryotic translation initiation factor 2 subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.178406 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: 33706
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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