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- PDB-2x7n: Mechanism of eIF6s anti-association activity -

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Basic information

Entry
Database: PDB / ID: 2x7n
TitleMechanism of eIF6s anti-association activity
Components
  • 60S RIBOSOMAL PROTEIN L23
  • 60S RIBOSOMAL PROTEIN L24-A
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 6
  • SARCIN-RICIN LOOP
KeywordsRIBOSOMAL PROTEIN/RNA / RIBOSOMAL PROTEIN-RNA COMPLEX / INITIATION FACTOR / PROTEIN BIOSYNTHESIS / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN
Function / homology
Function and homology information


maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal large subunit binding / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / preribosome, large subunit precursor / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal large subunit binding / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / preribosome, large subunit precursor / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal subunit export from nucleus / maturation of LSU-rRNA / translation initiation factor activity / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / translational initiation / rRNA processing / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / mRNA binding / nucleolus / RNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L14P, conserved site ...Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL14A / Eukaryotic translation initiation factor 6
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.8 Å
AuthorsGartmann, M. / Blau, M. / Armache, J.-P. / Mielke, T. / Topf, M. / Beckmann, R.
CitationJournal: J Biol Chem / Year: 2010
Title: Mechanism of eIF6-mediated inhibition of ribosomal subunit joining.
Authors: Marco Gartmann / Michael Blau / Jean-Paul Armache / Thorsten Mielke / Maya Topf / Roland Beckmann /
Abstract: During the process of ribosomal assembly, the essential eukaryotic translation initiation factor 6 (eIF6) is known to act as a ribosomal anti-association factor. However, a molecular understanding of ...During the process of ribosomal assembly, the essential eukaryotic translation initiation factor 6 (eIF6) is known to act as a ribosomal anti-association factor. However, a molecular understanding of the anti-association activity of eIF6 is still missing. Here we present the cryo-electron microscopy reconstruction of a complex of the large ribosomal subunit with eukaryotic eIF6 from Saccharomyces cerevisiae. The structure reveals that the eIF6 binding site involves mainly rpL23 (L14p in Escherichia coli). Based on our structural data, we propose that the mechanism of the anti-association activity of eIF6 is based on steric hindrance of intersubunit bridge formation around the dynamic bridge B6.
History
DepositionMar 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Derived calculations / Other / Version format compliance
Revision 1.2Aug 30, 2017Group: Data collection / Structure summary / Category: em_image_scans / entity / Item: _entity.src_method
Revision 1.3Oct 3, 2018Group: Data collection / Derived calculations / Category: em_software / ndb_struct_na_base_pair
Item: _em_software.image_processing_id / _ndb_struct_na_base_pair.propeller
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Assembly

Deposited unit
A: SARCIN-RICIN LOOP
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 6
C: 60S RIBOSOMAL PROTEIN L23
D: 60S RIBOSOMAL PROTEIN L24-A


Theoretical massNumber of molelcules
Total (without water)53,7974
Polymers53,7974
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-19 kcal/mol
Surface area22400 Å2
MethodPISA

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Components

#1: RNA chain SARCIN-RICIN LOOP


Mass: 9042.445 Da / Num. of mol.: 1 / Fragment: 2684-2711 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#2: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 6 / EIF-6


Mass: 24156.150 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-224 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q12522
#3: Protein 60S RIBOSOMAL PROTEIN L23 / YL32 / L17A


Mass: 14047.472 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-137 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04451, UniProt: P0CX41*PLUS
#4: Protein 60S RIBOSOMAL PROTEIN L24-A / L30 / YL221 / RP29


Mass: 6550.665 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-56 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04449

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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: 60S-EIF6 COMPLEX / Type: RIBOSOME / Details: CRYO-EM SINGLE-PARTICLE RECONSTRUCTION
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationCryogen name: ETHANE / Details: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38900 X / Cs: 2.26 mm
Specimen holderTemperature: 95 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: DEFOCUS GROUP VOLUMES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 11.8 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1705.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEX-EM
Atomic model buildingPDB-ID: 1G62

1g62


Accession code: 1G62 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 11.8 Å
Refinement stepCycle: LAST / Highest resolution: 11.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 600 0 0 3737

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