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- EMDB-10769: Structure of a human 48S translational initiation complex - eIF3 -

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Basic information

Entry
Database: EMDB / ID: EMD-10769
TitleStructure of a human 48S translational initiation complex - eIF3
Map data
Sample48S initiation complex
  • (Eukaryotic translation initiation factor 3 subunit ...) x 9
  • (40S ribosomal protein ...) x 10
Function / homology
Function and homology information


mRNA cap binding / cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / positive regulation of mRNA binding / IRES-dependent viral translational initiation / multi-eIF complex / cytoplasmic translational initiation ...mRNA cap binding / cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / positive regulation of mRNA binding / IRES-dependent viral translational initiation / multi-eIF complex / cytoplasmic translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / negative regulation of RNA splicing / eukaryotic 48S preinitiation complex / ubiquitin ligase inhibitor activity / laminin receptor activity / formation of cytoplasmic translation initiation complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / regulation of translational initiation / erythrocyte homeostasis / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / fibroblast growth factor binding / poly(U) RNA binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of ubiquitin-protein transferase activity / SRP-dependent cotranslational protein targeting to membrane / maturation of SSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of translational initiation / ribosomal small subunit biogenesis / translation initiation factor binding / viral transcription / thiol-dependent ubiquitin-specific protease activity / erythrocyte differentiation / laminin binding / translation initiation factor activity / translational initiation / polysomal ribosome / mRNA 3'-UTR binding / rough endoplasmic reticulum / microtubule organizing center / negative regulation of ERK1 and ERK2 cascade / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / metallopeptidase activity / positive regulation of translation / fibrillar center / neural tube closure / mRNA 5'-UTR binding / ubiquitinyl hydrolase 1 / rRNA processing / receptor tyrosine kinase binding / PML body / cytoplasmic translation / virus receptor activity / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / ribonucleoprotein complex / protein N-terminus binding / microtubule / protein stabilization / ribosome / structural constituent of ribosome / cell differentiation / postsynaptic density / protein deubiquitination / translation / cadherin binding / cell adhesion / mRNA binding / synapse / focal adhesion / nucleolus / positive regulation of gene expression / structural molecule activity / viral process / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / RNA binding / DNA binding / extracellular exosome / zinc ion binding / membrane / nucleoplasm / plasma membrane / nucleus / cytosol / cytoplasm
Ribosomal protein S5, C-terminal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S5, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Armadillo-type fold / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S2, conserved site / Zinc-binding ribosomal protein ...Ribosomal protein S5, C-terminal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S5, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Armadillo-type fold / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S2, conserved site / Zinc-binding ribosomal protein / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3Ae, conserved site / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Translation initiation factor 3 complex subunit L / Ribosomal protein S5 domain 2-type fold / Tetratricopeptide-like helical domain superfamily / Eukaryotic translation initiation factor 3 subunit K / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S5 / Ribosomal protein S11 / Ribosomal protein S21e / Ribosomal protein S2 / Ribosomal protein S3Ae / Ribosomal protein S17e / Ribosomal protein S26e / Proteasome component (PCI) domain / S15/NS1, RNA-binding / Ribosomal protein S27e / Ribosomal protein S15 / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal protein S7e / Ribosomal protein S5, eukaryotic/archaeal / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Ribosomal protein S15P / Ribosomal S11, conserved site / Rpn11/EIF3F, C-terminal / Winged helix-like DNA-binding domain superfamily / 40S ribosomal protein SA, C-terminal domain / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit M / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Eukaryotic translation initiation factor 3 subunit H / Ribosomal protein S11 superfamily / MPN domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S26e superfamily / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e superfamily / eIF3 subunit M, C-terminal helix domain / CSN8/PSMD8/EIF3K
Eukaryotic translation initiation factor 3 subunit F / 40S ribosomal protein S14 / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein S21 / 40S ribosomal protein S26 / 40S ribosomal protein S13 / 40S ribosomal protein S7 ...Eukaryotic translation initiation factor 3 subunit F / 40S ribosomal protein S14 / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein S21 / 40S ribosomal protein S26 / 40S ribosomal protein S13 / 40S ribosomal protein S7 / Eukaryotic translation initiation factor 3 subunit D / 40S ribosomal protein S3a / Eukaryotic translation initiation factor 3 subunit E / 40S ribosomal protein S27 / 40S ribosomal protein S2 / 40S ribosomal protein SA / 40S ribosomal protein S17 / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit L
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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: 6ybd

SummaryFull reportAbout validation report
History
DepositionMar 16, 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: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ybd
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ybd
  • 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_10769.map.gz / Format: CCP4 / Size: 83.7 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 280 pix.
= 300.72 Å
1.07 Å/pix.
x 280 pix.
= 300.72 Å
1.07 Å/pix.
x 280 pix.
= 300.72 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: 0.04
Minimum - Maximum-0.18092114 - 0.29472923
Average (Standard dev.)0.0009115565 (±0.00900954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 300.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z300.720300.720300.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1810.2950.001

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Supplemental data

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Segmentation: #1

Fileemd_10769_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_10769_additional.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_10769_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_10769_half_map_2.map
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Sample components

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Entire 48S initiation complex

EntireName: 48S initiation complex / Number of components: 20

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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 3 subunit M

ProteinName: Eukaryotic translation initiation factor 3 subunit M / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.555832 kDa
SourceSpecies: Human (human)

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

ProteinName: Eukaryotic translation initiation factor 3 subunit F / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.593645 kDa
SourceSpecies: Human (human)

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

ProteinName: Eukaryotic translation initiation factor 3 subunit A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 166.903781 kDa
SourceSpecies: Human (human)

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Component #5: protein, Eukaryotic translation initiation factor 3 subunit E

ProteinName: Eukaryotic translation initiation factor 3 subunit E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.281633 kDa
SourceSpecies: Human (human)

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

ProteinName: Eukaryotic translation initiation factor 3 subunit C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.503945 kDa
SourceSpecies: Human (human)

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Component #7: protein, Eukaryotic translation initiation factor 3 subunit H

ProteinName: Eukaryotic translation initiation factor 3 subunit H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.979277 kDa
SourceSpecies: Human (human)

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Component #8: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Human (human)

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Component #9: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.480186 kDa
SourceSpecies: Human (human)

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Component #10: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Human (human)

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Component #11: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.578156 kDa
SourceSpecies: Human (human)

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Component #12: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.376516 kDa
SourceSpecies: Human (human)

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Component #13: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.002061 kDa
SourceSpecies: Human (human)

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Component #14: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.883938 kDa
SourceSpecies: Human (human)

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Component #15: protein, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.047532 kDa
SourceSpecies: Human (human)

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Component #16: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.302772 kDa
SourceSpecies: Human (human)

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Component #17: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.259389 kDa
SourceSpecies: Human (human)

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Component #18: protein, Eukaryotic translation initiation factor 3 subunit D

ProteinName: Eukaryotic translation initiation factor 3 subunit D / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.060758 kDa
SourceSpecies: Human (human)

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Component #19: protein, Eukaryotic translation initiation factor 3 subunit K

ProteinName: Eukaryotic translation initiation factor 3 subunit K / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.083619 kDa
SourceSpecies: Human (human)

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Component #20: protein, Eukaryotic translation initiation factor 3 subunit L

ProteinName: Eukaryotic translation initiation factor 3 subunit L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.803734 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: 11882
3D reconstructionResolution: 3.3 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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