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- PDB-1trj: Homology Model of Yeast RACK1 Protein fitted into 11.7A cryo-EM m... -

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Basic information

Entry
Database: PDB / ID: 1trj
TitleHomology Model of Yeast RACK1 Protein fitted into 11.7A cryo-EM map of Yeast 80S Ribosome
Components
  • Guanine nucleotide-binding protein beta subunit-like protein
  • Helix 39 of 18S rRNA
  • Helix 40 of 18S rRNA
KeywordsSIGNALING PROTEIN / RACK1 / Ribosome / homology model
Function / homology
Function and homology information


regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / mRNA destabilization / negative regulation of translational frameshifting / G-protein alpha-subunit binding / translation regulator activity / rescue of stalled ribosome ...regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / mRNA destabilization / negative regulation of translational frameshifting / G-protein alpha-subunit binding / translation regulator activity / rescue of stalled ribosome / protein kinase C binding / maintenance of translational fidelity / ribosome binding / cytosolic small ribosomal subunit / cytoplasmic translation / negative regulation of translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / nucleus / cytoplasm / cytosol
Similarity search - Function
Small (40S) ribosomal subunit Asc1/RACK1 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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
RNA / RNA (> 10) / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 Å
AuthorsSengupta, J. / Nilsson, J. / Gursky, R. / Spahn, C.M. / Nissen, P. / Frank, J.
Citation
Journal: Nat Struct Mol Biol / Year: 2004
Title: Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM.
Authors: Jayati Sengupta / Jakob Nilsson / Richard Gursky / Christian M T Spahn / Poul Nissen / Joachim Frank /
Abstract: RACK1 serves as a scaffold protein for a wide range of kinases and membrane-bound receptors. It is a WD-repeat family protein and is predicted to have a beta-propeller architecture with seven blades ...RACK1 serves as a scaffold protein for a wide range of kinases and membrane-bound receptors. It is a WD-repeat family protein and is predicted to have a beta-propeller architecture with seven blades like a Gbeta protein. Mass spectrometry studies have identified its association with the small subunit of eukaryotic ribosomes and, most recently, it has been shown to regulate initiation by recruiting protein kinase C to the 40S subunit. Here we present the results of a cryo-EM study of the 80S ribosome that positively locate RACK1 on the head region of the 40S subunit, in the immediate vicinity of the mRNA exit channel. One face of RACK1 exposes the WD-repeats as a platform for interactions with kinases and receptors. Using this platform, RACK1 can recruit other proteins to the ribosome.
#1: Journal: Nature / Year: 2003
Title: Release of eIF6 (p27BBP) from the 60S subunit allows 80S ribosome assembly
Authors: Ceci, M. / Gaviraghi, C. / Gorrini, C. / Sala, L.A. / Offenhauser, N. / Marchisio, P.C. / Biffo, S.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Cpc2/RACK1 is a ribosome-associated protein that promotes efficient translation in Schizosaccharomyces pombe
Authors: Shor, B. / Calaycay, J. / Rushbrook, J. / McLeod, M.
#3: Journal: Biochem.J. / Year: 2004
Title: Asc1p, a WD40-domain containing adaptor protein, is required for the interaction of the RNA-binding protein Scp160p with polysomes
Authors: Baum, S. / Bittins, M. / Frey, S. / Seedorf, M.
History
DepositionJun 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE ONLY COORDINATES FOR CA ATOMS FROM THE PROTEIN AND P ATOMS FROM THE NUCLEIC ACIDS WERE ...SEQUENCE ONLY COORDINATES FOR CA ATOMS FROM THE PROTEIN AND P ATOMS FROM THE NUCLEIC ACIDS WERE INCLUDED IN THE STRUCTURE.

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Assembly

Deposited unit
B: Helix 39 of 18S rRNA
C: Helix 40 of 18S rRNA
A: Guanine nucleotide-binding protein beta subunit-like protein


Theoretical massNumber of molelcules
Total (without water)56,3493
Polymers56,3493
Non-polymers00
Water00
1


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

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Components

#1: RNA chain Helix 39 of 18S rRNA / Coordinate model: P atoms only


Mass: 13155.822 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain Helix 40 of 18S rRNA / Coordinate model: P atoms only


Mass: 8868.415 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Guanine nucleotide-binding protein beta subunit-like protein / RACK1 protein / Coordinate model: Cα atoms only


Mass: 34324.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011

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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: 80S ribosome / Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: QUANTIFOIL HOLLEY CARBON FILM GRIDS
VitrificationCryogen name: ETHANE / Details: RAPID-FREEZING IN LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20 / Date: Feb 1, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 52000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 4900 nm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: CTF CORRECTION OF 3D MAPS BY WIENER FILTERATION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D PROJECTION MATCHING GRADIENT WITH REGULARIZATION / Resolution: 11.7 Å / Actual pixel size: 2.93 Å / Magnification calibration: TMV / Details: SPIDER PACKAGE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: METHOD--USING A RAPID MOTIF SEARCH MODULE OF SPIDER (THE CRYO-EM MAP USED FOR FITTING WAS INTERPOLATED TO PIXEL SIZE 2.82)
RefinementHighest resolution: 11.7 Å
Refinement stepCycle: LAST / Highest resolution: 11.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms314 68 0 0 382

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