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- EMDB-3056: Structure of mammalian eIF3 in the context of the 43S preinitiati... -

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Basic information

Entry
Database: EMDB / ID: EMD-3056
TitleStructure of mammalian eIF3 in the context of the 43S preinitiation complex
Map dataReconstruction of eIF3 octamer core
Sample
  • Sample: eIF3 octamer core of Rabbit eIF3
  • 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: eukaryotic initiation factor 1
  • Protein or peptide: eukaryotic initiation factor 1A
  • RNA: initiator transfer RNA
KeywordseIF3 / eukaryotic Initiation Factor 3 / preinitiation complex / PCI/MPN core / eIF3g/i/b / eIF3d
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein deubiquitination / translation initiation factor binding / translation initiation factor activity / positive regulation of translation / PML body / fibrillar center / metallopeptidase activity / ribosome binding / cysteine-type deubiquitinase activity / postsynaptic density / synapse / nucleolus / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / 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 / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal ...Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / 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 / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / 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 A / 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. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit L / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit F
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 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) releaseJul 8, 2015-
Map releaseSep 9, 2015-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5a5t
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3056.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of eIF3 octamer core
Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.06188392 - 0.12141231
Average (Standard dev.)0.00010273 (±0.00224358)
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-0.0620.1210.000

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Supplemental data

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Sample components

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Entire : eIF3 octamer core of Rabbit eIF3

EntireName: eIF3 octamer core of Rabbit eIF3
Components
  • Sample: eIF3 octamer core of Rabbit eIF3
  • 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: eukaryotic initiation factor 1
  • Protein or peptide: eukaryotic initiation factor 1A
  • RNA: initiator transfer RNA

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Supramolecule #1000: eIF3 octamer core of Rabbit eIF3

SupramoleculeName: eIF3 octamer core of Rabbit eIF3 / type: sample / ID: 1000
Details: The sample was monodisperse, eIF3 octamer core was locally refined from a reconstruction of the mammalian 43S preinitiation complex
Oligomeric state: One octamer / Number unique components: 7
Molecular weightExperimental: 450 KDa / Theoretical: 450 KDa

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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 / Number of copies: 1 / 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 / Number of copies: 1 / 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 #4: DHX29

MacromoleculeName: DHX29 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm

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Macromolecule #5: eukaryotic initiation factor 1

MacromoleculeName: eukaryotic initiation factor 1 / type: protein_or_peptide / ID: 5 / Name.synonym: eIF1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm

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Macromolecule #6: eukaryotic initiation factor 1A

MacromoleculeName: eukaryotic initiation factor 1A / type: protein_or_peptide / ID: 6 / Name.synonym: eIF3e / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm

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Macromolecule #3: initiator transfer RNA

MacromoleculeName: initiator transfer RNA / type: rna / ID: 3 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30120 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: PHILIPS ROTATION HOLDER
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 / Number real images: 8000 / Average electron dose: 25 e/Å2
Tilt angle min0
Tilt angle max0
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: 6.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 87192

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