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- PDB-5a5t: Structure of mammalian eIF3 in the context of the 43S preinitiati... -

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Basic information

Entry
Database: PDB / ID: 5a5t
TitleStructure of mammalian eIF3 in the context of the 43S preinitiation complex
Components
  • (EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT ...Eukaryotic initiation factor 3) x 7
  • UNCHARACTERIZED PROTEIN
KeywordsHYDROLASE / EIF3 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 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: em_software / Item: _em_software.image_processing_id / _em_software.name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3056
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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F
H: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H
K: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K
L: UNCHARACTERIZED PROTEIN
M: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M


Theoretical massNumber of molelcules
Total (without water)527,3978
Polymers527,3978
Non-polymers00
Water0
1


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

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Components

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EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT ... , 7 types, 7 molecules ACEFHKM

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A / Eukaryotic initiation factor 3 / EIF3A / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 10 / EIF-3-THETA


Mass: 164902.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SMZ5
#2: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C / Eukaryotic initiation factor 3 / EIF3C / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 8 / EIF3 P110


Mass: 97923.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1U971
#3: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E / Eukaryotic initiation factor 3 / EIF3E / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 6 / EIF-3 P48


Mass: 52281.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SUC8
#4: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F / Eukaryotic initiation factor 3 / EIF3F / DEUBIQUITINATING ENZYME EIF3F / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 5 / EIF- ...EIF3F / DEUBIQUITINATING ENZYME EIF3F / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 5 / EIF-3-EPSILON / EIF3 P47


Mass: 37846.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: U3KNL5, ubiquitinyl hydrolase 1
#5: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H / Eukaryotic initiation factor 3 / EIF3H / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 3 / EIF-3-GAMMA / EIF3 P40 SUBUNIT


Mass: 39952.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1ST95
#6: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K / Eukaryotic initiation factor 3 / EIF3K / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 12 / EIF-3 P25


Mass: 25129.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1T3L2
#8: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M / Eukaryotic initiation factor 3 / EIF3M / FETAL LUNG PROTEIN B5 / HFL-B5 / PCI DOMAIN-CONTAINING PROTEIN 1


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SLW8

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Protein , 1 types, 1 molecules L

#7: Protein UNCHARACTERIZED PROTEIN


Mass: 66804.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SED9

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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: EIF3 OCTAMER CORE OF RABBIT EIF3 / Type: COMPLEX
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 FIELDBright-field microscopy / 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: 6 Å / Num. of particles: 87192 / Actual pixel size: 1.66 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3056. (DEPOSITION ID: 13501).
Symmetry type: POINT
RefinementHighest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25432 0 0 0 25432

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