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Yorodumi- PDB-5a5u: Structure of mammalian eIF3 in the context of the 43S preinitiati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a5u | ||||||
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Title | Structure of mammalian eIF3 in the context of the 43S preinitiation complex | ||||||
Components |
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Keywords | TRANSLATION / 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 / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / 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 | ||||||
Biological species | ORYCTOLAGUS CUNICULUS (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | ||||||
Authors | des-Georges, A. / Dhote, V. / Kuhn, L. / Hellen, C.U.T. / Pestova, T.V. / Frank, J. / Hashem, Y. | ||||||
Citation | Journal: 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 |
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-Structure visualization
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Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 5a5u.cif.gz | 208.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a5u.ent.gz | 154 KB | Display | PDB format |
PDBx/mmJSON format | 5a5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a5u_validation.pdf.gz | 766.9 KB | Display | wwPDB validaton report |
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Full document | 5a5u_full_validation.pdf.gz | 785.5 KB | Display | |
Data in XML | 5a5u_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 5a5u_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/5a5u ftp://data.pdbj.org/pub/pdb/validation_reports/a5/5a5u | HTTPS FTP |
-Related structure data
Related structure data | 3057MC 3056C 3058C 5a5tC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell: RETICULCYTES / Tissue: BLOOD |
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#2: Protein | 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 | 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 details | THE SAMPLE OF CHAIN B CONTAINS FULL LENGTH EIF3B. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MAMMALIAN 43S PREINITIATION COMPLEX BOUND TO DHX29 / Type: RIBOSOME |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/HE / Date: Nov 1, 2013 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 30120 X / Nominal defocus max: 4500 nm / Nominal defocus min: 500 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
-Processing
EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: TEMPLATE MATCHING / Resolution: 9 Å / Num. of particles: 54410 Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3057. Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 9 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9 Å
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