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- PDB-5ydt: Remodeled Utp30 in 90S pre-ribosome (Mtr4-depleted, Enp1-TAP) -

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Basic information

Entry
Database: PDB / ID: 5ydt
TitleRemodeled Utp30 in 90S pre-ribosome (Mtr4-depleted, Enp1-TAP)
Components
  • 5' ETS RNA
  • Ribosome biogenesis protein UTP30
  • Saccharomyces cerevisiae strain ALI 308 18S ribosomal RNA gene, partial sequence
  • Unassigned helices
KeywordsRIBOSOME / ribosome assembly / 90S pre-ribosome
Function / homology
Function and homology information


90S preribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / small-subunit processome / ribosomal small subunit biogenesis / cytosolic large ribosomal subunit / nucleolus / RNA binding / nucleus
Similarity search - Function
Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Ribosome biogenesis protein UTP30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYe, K. / Zhu, X. / Hu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China91540201 China
CitationJournal: 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.
History
DepositionSep 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 28, 2018Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.pdb_format_compatible
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
U5: Ribosome biogenesis protein UTP30
SA: Saccharomyces cerevisiae strain ALI 308 18S ribosomal RNA gene, partial sequence
5A: 5' ETS RNA
UC: Unassigned helices


Theoretical massNumber of molelcules
Total (without water)61,2264
Polymers61,2264
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Ribosome biogenesis protein UTP30 / / U3 snoRNP-associated protein UTP30


Mass: 31668.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36144
#2: RNA chain Saccharomyces cerevisiae strain ALI 308 18S ribosomal RNA gene, partial sequence / 18S ribosomal RNA


Mass: 20614.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 33334408
#3: RNA chain 5' ETS RNA


Mass: 6031.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#4: Protein/peptide Unassigned helices


Mass: 2911.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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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: 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: RELION / Version: 1.4 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73543 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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