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- PDB-5ydu: Crystal structure of Utp30 -

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Basic information

Entry
Database: PDB / ID: 5ydu
TitleCrystal structure of Utp30
ComponentsRibosome biogenesis protein UTP30
KeywordsRIBOSOMAL PROTEIN / ribosome assembly / 90S pre-ribosome
Function / homology
Function and homology information


90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of SSU-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
PHOSPHATE ION / Ribosome biogenesis protein UTP30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.646 Å
AuthorsHu, J. / Zhu, X. / Ye, K.
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 1.2Mar 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome biogenesis protein UTP30
B: Ribosome biogenesis protein UTP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4333
Polymers63,3382
Non-polymers951
Water27015
1
A: Ribosome biogenesis protein UTP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7642
Polymers31,6691
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosome biogenesis protein UTP30


Theoretical massNumber of molelcules
Total (without water)31,6691
Polymers31,6691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.364, 90.880, 157.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 31668.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: UTP30, YKR060W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36144
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.45 M tri-sodium citrate dehydrate and 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.646→50 Å / Num. obs: 15291 / % possible obs: 98.7 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 21.4
Reflection shellResolution: 2.646→2.7 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2 / Num. unique obs: 1432 / CC1/2: 0.768 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.646→45.939 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 756 4.95 %
Rwork0.2003 --
obs0.2036 15282 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.646→45.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 5 15 3897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093944
X-RAY DIFFRACTIONf_angle_d1.0815303
X-RAY DIFFRACTIONf_dihedral_angle_d19.0962482
X-RAY DIFFRACTIONf_chiral_restr0.057610
X-RAY DIFFRACTIONf_plane_restr0.007664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6459-2.85020.3591380.27422756X-RAY DIFFRACTION95
2.8502-3.13690.41281570.26392859X-RAY DIFFRACTION99
3.1369-3.59070.31141580.2192901X-RAY DIFFRACTION99
3.5907-4.52330.24361470.18232950X-RAY DIFFRACTION100
4.5233-45.9460.19741560.17143060X-RAY DIFFRACTION100

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