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- SASDBG6: Ribosome biogenesis protein 15 (Nop15) (Ribosome biogenesis prote... -

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Basic information

Entry
Database: SASBDB / ID: SASDBG6
SampleRibosome biogenesis protein 15 (Nop15)
  • Ribosome biogenesis protein 15 (protein), Nop15, Saccharomyces cerevisiae
Function / homology
Function and homology information


preribosome, large subunit precursor / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / rRNA binding / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Ribosome biogenesis protein 15, RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Ribosome biogenesis protein 15
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate.
Authors: Jun Zhang / Lauren E Gonzalez / Traci M Tanaka Hall /
Abstract: The RNA recognition motif (RRM) is the most abundant RNA-binding domain in eukaryotes, and it plays versatile roles in RNA metabolism. Despite its abundance, diversity of RRM structure and function ...The RNA recognition motif (RRM) is the most abundant RNA-binding domain in eukaryotes, and it plays versatile roles in RNA metabolism. Despite its abundance, diversity of RRM structure and function is generated by variations on a conserved core. Yeast Nop15 is an RRM protein that is essential for large ribosomal subunit biogenesis. We determined a 2.0 Å crystal structure of Nop15 that reveals a C-terminal α-helical region obscures its canonical RNA-binding surface. Small-angle X-ray scattering, NMR and RNA-binding analyses further reveal that the C-terminal residues of Nop15 are highly flexible, but essential for tight RNA binding. Moreover, comparison with a recently reported cryo-electron microscopy structure indicates that dramatic rearrangement of the C-terminal region of Nop15 in the pre-ribosome exposes the RNA-binding surface to recognize the base of its stem-loop target RNA and extends a newly-formed α helix to the distal loop where it forms protein interactions.
Contact author
  • Jun Zhang (NIH, National Institutes of Health, Bethesda, MD, Bethesda, Maryland, USA)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #636
Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 0.649
Search similar-shape structures of this assembly by Omokage search (details)
Model #637
Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 0.649
Search similar-shape structures of this assembly by Omokage search (details)
Model #638
Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 0.649
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Ribosome biogenesis protein 15 (Nop15) / Specimen concentration: 0.70-3.00
BufferName: 25 mM HEPES, 500 mM NaCl, 2 mM DTT / pH: 7.5
Entity #402Name: Nop15 / Type: protein / Description: Ribosome biogenesis protein 15 / Formula weight: 16.541 / Num. of mol.: 1 / Source: Saccharomyces cerevisiae / References: UniProt: P53927
Sequence:
KDKKTLEEYS GIIYVSRLPH GFHEKELSKY FAQFGDLKEV RLARNKKTGN SRHYGFLEFV NKEDAMIAQE SMNNYLLMGH LLQVRVLPKG AKIEKLYKYK KRVLVEKGIT KPVKQLKDNM KQKHEERIKK LAKSGIEFKW

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Experimental information

BeamInstrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS)
City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1 Å
DetectorName: MAR 165 CCD
Scan
Title: Ribosome biogenesis protein 15 / Measurement date: Apr 25, 2013 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 0.5 sec. / Number of frames: 1 / Unit: 1/A /
MinMax
Q0.0198 0.2934
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 396 /
MinMax
Q0.035575 0.275763
P(R) point1 396
R0 103
Result
Type of curve: single_conc /
ExperimentalPorod
MW16.4 kDa23 kDa
Volume-38 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I0125.6 3.5 113.76 3.6
Radius of gyration, Rg2.86 nm0.09 2.4 nm0.09

MinMax
D-10.3
Guinier point27 56

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