|Entry||Database: PDB / ID: 5ydt|
|Title||Remodeled Utp30 in 90S pre-ribosome (Mtr4-depleted, Enp1-TAP)|
|Keywords||RIBOSOME / ribosome assembly / 90S pre-ribosome|
|Function / homology||Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 90S preribosome / ribosomal small subunit biogenesis / maturation of LSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleolus / RNA binding / Ribosome biogenesis protein UTP30 / gb:33334408: |
Function and homology information
|Specimen source||Saccharomyces cerevisiae (baker's yeast)|
Saccharomyces cerevisiae S288c (yeast)
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution|
|Authors||Ye, K. / Zhu, X. / Hu, J.|
|Citation||Journal: RNA / Year: 2017|
Title: Structure and RNA recognition of ribosome assembly factor Utp30.
Authors: Jianfei Hu / Xing Zhu / Keqiong Ye
Abstract: The 90S preribosomes are gigantic early assembly intermediates of small ribosomal subunits. Cryo-EM structures of 90S were recently determined, but many of its components have not been accurately ...The 90S preribosomes are gigantic early assembly intermediates of small ribosomal subunits. Cryo-EM structures of 90S were recently determined, but many of its components have not been accurately modeled. Here we determine the crystal structure of yeast Utp30, a ribosomal L1 domain-containing protein in 90S, at 2.65 Å resolution, revealing a classic two-domain fold. The structure of Utp30 fits well into the cryo-EM density of 90S, confirming its previously assigned location. Utp30 binds to the rearranged helix 41 of 18S rRNA and helix 4 of 5' external transcribed spacer in 90S. Comparison of RNA-binding modes of different L1 domains illustrates that they consistently recognize a short RNA duplex with the concaved surface of domain I, but are versatile in RNA recognition outside the core interface. Cic1 is a paralog of Utp30 associating with large subunit preribosomes. Utp30 and Cic1 share similar RNA-binding modes, suggesting that their distinct functions may be executed by a single protein in other organisms. Deletion of Utp30 does not affect the composition of 90S. The nonessential role of Utp30 could be ascribed to its peripheral localization and redundant interactions in 90S.
SummaryFull reportAbout validation report
|Date||Deposition: Sep 14, 2017 / Release: Nov 1, 2017|
|Structure viewer||Molecule: |
Downloads & links
U5: Ribosome biogenesis protein UTP30
SA: Saccharomyces cerevisiae strain ALI 308 18S ribosomal RNA gene, partial sequence
5A: 5' ETS RNA
UC: Unassigned helices
|#1: Protein/peptide|| |
Mass: 31668.939 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36144
|#2: RNA chain|| |
Mass: 20614.229 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 33334408
|#3: RNA chain|| |
Mass: 6031.593 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
|#4: Protein/peptide|| |
Mass: 2911.580 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)|
Type: RIBOSOME / Entity ID: 1,
|Molecular weight||Experimental value: NO||Source (natural)||Organism: Saccharomyces cerevisiae S288c (yeast)||Buffer solution||pH: 8||Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES||Vitrification||Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)|
|EM software||Name: RELION / Version: 1.4 / Category: 3D reconstruction|
|CTF correction||Type: PHASE FLIPPING ONLY|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 73543 / Symmetry type: POINT|
|Atomic model building||Ref space: REAL|
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