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- EMDB-3057: Structure of mammalian eIF3 in the context of the 43S preinitiati... -

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Entry
Database: EMDB / ID: EMD-3057
TitleStructure of mammalian eIF3 in the context of the 43S preinitiation complex
Map dataReconstruction of mammalian preinitiation complex after focused classification on the eIF3g/i/b peripheral subunits complex of eIF3
Sample
  • Sample: Mammalian 43S preinitiation complex bound to DHX29
  • Complex: 40S small ribosomal subunit
  • Protein or peptide: eukaryotic initiation factor 3
  • Protein or peptide: eukaryotic initiation factor 2
  • Protein or peptide: DHX29
  • Protein or peptide: eIF1
  • Protein or peptide: eIF1A
  • RNA: initiator transfer RNA
KeywordseIF3 / eIF3 octamer core / mammalian preinitiation 34S complex / eIF3g/i/b / eIF3d
Function / homology
Function and homology information


organelle / viral translational termination-reinitiation / translation activator activity / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex ...organelle / viral translational termination-reinitiation / translation activator activity / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / cellular response to chemical stress / regulation of translational initiation / protein-synthesizing GTPase / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / metal-dependent deubiquitinase activity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cytoplasmic translational initiation / laminin receptor activity / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / positive regulation of translational initiation / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / regulation of translational fidelity / phagocytic cup / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / laminin binding / translation initiation factor binding / gastrulation / translation initiation factor activity / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / response to endoplasmic reticulum stress / DNA-(apurinic or apyrimidinic site) lyase / helicase activity / ribosome assembly / positive regulation of translation / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / PML body / spindle / fibrillar center / cytoplasmic stress granule / rRNA processing / ribonucleoside triphosphate phosphatase activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / ribosomal small subunit assembly / virus receptor activity / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / cell differentiation / tRNA binding / cysteine-type deubiquitinase activity / RNA helicase activity / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / RNA helicase / ribosome / cadherin binding / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / GTPase activity / apoptotic process / centrosome / synapse / dendrite / GTP binding / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / DNA binding
Similarity search - Function
ATP-dependent RNA helicase DHX29 / : / : / ATP-dependent RNA helicase DHX29, DSRM-like / ATP-dependent RNA helicase DHX29, UBA domain / EIF3I / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H ...ATP-dependent RNA helicase DHX29 / : / : / ATP-dependent RNA helicase DHX29, DSRM-like / ATP-dependent RNA helicase DHX29, UBA domain / EIF3I / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor, beta propellor-like domain / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / : / Eukaryotic translation initiation factor eIF2A / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / EIF3CL-like, C-terminal domain / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / : / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / : / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Six-bladed beta-propeller, TolB-like / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / S1 domain profile. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Translation elongation factor EFTu-like, domain 2 / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / S27a-like superfamily / 40S Ribosomal protein S10 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Elongation factor Tu domain 2 / Plectin/S10, N-terminal
Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit H / protein-synthesizing GTPase / Small ribosomal subunit protein uS4 / Eukaryotic translation initiation factor 3 subunit L / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 ...Small ribosomal subunit protein eS32 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit H / protein-synthesizing GTPase / Small ribosomal subunit protein uS4 / Eukaryotic translation initiation factor 3 subunit L / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit M / Small ribosomal subunit protein uS15 / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit E / Small ribosomal subunit protein eS7 / Eukaryotic translation initiation factor 3 subunit B / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 3 subunit K / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit I / ATP-dependent RNA helicase DHX29 / Small ribosomal subunit protein uS7
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
Authorsdes-Georges A / Dhote V / Kuhn L / Hellen CUT / Pestova TV / Frank J / Hashem Y
CitationJournal: Nature / Year: 2015
Title: Structure of mammalian eIF3 in the context of the 43S preinitiation complex.
Authors: Amedee des Georges / Vidya Dhote / Lauriane Kuhn / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank / Yaser Hashem /
Abstract: During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of ...During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of messenger RNA and scan along it to the initiation codon. Scanning on structured mRNAs also requires the DExH-box protein DHX29. Mammalian eIF3 contains 13 subunits and participates in nearly all steps of translation initiation. Eight subunits having PCI (proteasome, COP9 signalosome, eIF3) or MPN (Mpr1, Pad1, amino-terminal) domains constitute the structural core of eIF3, to which five peripheral subunits are flexibly linked. Here we present a cryo-electron microscopy structure of eIF3 in the context of the DHX29-bound 43S complex, showing the PCI/MPN core at ∼6 Å resolution. It reveals the organization of the individual subunits and their interactions with components of the 43S complex. We were able to build near-complete polyalanine-level models of the eIF3 PCI/MPN core and of two peripheral subunits. The implications for understanding mRNA ribosomal attachment and scanning are discussed.
History
DepositionJun 21, 2015-
Header (metadata) releaseAug 5, 2015-
Map releaseSep 9, 2015-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: PDBe / Status: Released

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Structure visualization

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  • Atomic models: PDB-5a5u
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5a5u
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Structure viewerEM map:
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Supplemental images

EMD-3057_ima...

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Map

FileDownload / File: emd_3057.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of mammalian preinitiation complex after focused classification on the eIF3g/i/b peripheral subunits complex of eIF3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 300 pix.
= 498. Å		1.66 Å/pix.
x 300 pix.
= 498. Å		1.66 Å/pix.
x 300 pix.
= 498. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.26261827 - 0.40436754
Average (Standard dev.)0.00070926 (±0.01986324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.661.661.66
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z498.000498.000498.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2630.4040.001

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Supplemental data

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Sample components

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Entire : Mammalian 43S preinitiation complex bound to DHX29

EntireName: Mammalian 43S preinitiation complex bound to DHX29
Components
  • Sample: Mammalian 43S preinitiation complex bound to DHX29
  • Complex: 40S small ribosomal subunit
  • Protein or peptide: eukaryotic initiation factor 3
  • Protein or peptide: eukaryotic initiation factor 2
  • Protein or peptide: DHX29
  • Protein or peptide: eIF1
  • Protein or peptide: eIF1A
  • RNA: initiator transfer RNA

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Supramolecule #1000: Mammalian 43S preinitiation complex bound to DHX29

SupramoleculeName: Mammalian 43S preinitiation complex bound to DHX29 / type: sample / ID: 1000 / Number unique components: 7

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Supramolecule #1: 40S small ribosomal subunit

SupramoleculeName: 40S small ribosomal subunit / type: complex / ID: 1 / Name.synonym: SSU / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm

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Macromolecule #1: eukaryotic initiation factor 3

MacromoleculeName: eukaryotic initiation factor 3 / type: protein_or_peptide / ID: 1 / Name.synonym: eIF3 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm

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Macromolecule #2: eukaryotic initiation factor 2

MacromoleculeName: eukaryotic initiation factor 2 / type: protein_or_peptide / ID: 2 / Name.synonym: eIF2 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm

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Macromolecule #3: DHX29

MacromoleculeName: DHX29 / type: protein_or_peptide / ID: 3 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pQ31

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Macromolecule #4: eIF1

MacromoleculeName: eIF1 / type: protein_or_peptide / ID: 4 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pQ31

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Macromolecule #5: eIF1A

MacromoleculeName: eIF1A / type: protein_or_peptide / ID: 5 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pQ31

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Macromolecule #6: initiator transfer RNA

MacromoleculeName: initiator transfer RNA / type: rna / ID: 6 / Name.synonym: tRNAiMet / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 105 K / Average: 100 K
DateNov 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 6.35 µm / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30120 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: GATAN HELIUM
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 54410

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