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- PDB-5a5u: Structure of mammalian eIF3 in the context of the 43S preinitiati... -

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Basic information

Entry
Database: PDB / ID: 5a5u
TitleStructure of mammalian eIF3 in the context of the 43S preinitiation complex
Components
  • EUKARYOTIC INITIATION FACTOR 3
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
KeywordsTRANSLATION / EIF3 / EIF3 OCTAMER CORE / MAMMALIAN PREINITIATION 34S COMPLEX / EIF3G/I/B / EIF3D
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / cytoplasmic translational initiation / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / cytoplasmic translational initiation / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding / translation initiation factor activity / translational initiation / cytoplasmic stress granule / RNA binding
Similarity search - Function
EIF3I / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / Six-bladed beta-propeller, TolB-like / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...EIF3I / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / Six-bladed beta-propeller, TolB-like / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
Authorsdes-Georges, A. / Dhote, V. / Kuhn, L. / Hellen, C.U.T. / Pestova, T.V. / 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, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_image_scans
Revision 1.4Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id / _em_software.name
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: EUKARYOTIC INITIATION FACTOR 3
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
I: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I


Theoretical massNumber of molelcules
Total (without water)167,8193
Polymers167,8193
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein EUKARYOTIC INITIATION FACTOR 3


Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell: RETICULCYTES / Tissue: BLOOD
#2: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B / EUKARYOTIC INITIATION FACTOR 3


Mass: 124402.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SZ03
#3: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I / EIF3I / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 39 KDA SUBUNIT / EIF-3 39 KDA SUBUNIT / EIF3 P39 ...EIF3I / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 39 KDA SUBUNIT / EIF-3 39 KDA SUBUNIT / EIF3 P39 / EUKARYOTIC INITIATION FACTOR 3


Mass: 38803.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell: RETICULCYTES / Tissue: BLOOD / References: UniProt: P40217
Sequence detailsTHE SAMPLE OF CHAIN B CONTAINS FULL LENGTH EIF3B.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MAMMALIAN 43S PREINITIATION COMPLEX BOUND TO DHX29 / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV,

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE / Date: Nov 1, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 30120 X / Nominal defocus max: 4500 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: TEMPLATE MATCHING / Resolution: 9 Å / Num. of particles: 54410
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3057.
Symmetry type: POINT
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8124 0 0 0 8124

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