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- PDB-5t9p: Structural analysis reveals the flexible C-terminus of Nop15 unde... -

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Basic information

Entry
Database: PDB / ID: 5t9p
TitleStructural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate
ComponentsRibosome biogenesis protein 15
KeywordsRIBOSOMAL PROTEIN / Nop15 / RRM
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, J. / Gonzalez, E.L. / Hall, M.T.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105404 United States
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.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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
B: Ribosome biogenesis protein 15
C: Ribosome biogenesis protein 15
A: Ribosome biogenesis protein 15
D: Ribosome biogenesis protein 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,49822
Polymers52,1934
Non-polymers1,30518
Water4,378243
1
B: Ribosome biogenesis protein 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,67010
Polymers13,0481
Non-polymers6229
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ribosome biogenesis protein 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5037
Polymers13,0481
Non-polymers4556
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ribosome biogenesis protein 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1442
Polymers13,0481
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribosome biogenesis protein 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1803
Polymers13,0481
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Ribosome biogenesis protein 15
A: Ribosome biogenesis protein 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,81512
Polymers26,0972
Non-polymers71810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-97 kcal/mol
Surface area10980 Å2
MethodPISA
6
C: Ribosome biogenesis protein 15
D: Ribosome biogenesis protein 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,68310
Polymers26,0972
Non-polymers5878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-114 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.242, 157.399, 47.130
Angle α, β, γ (deg.)90.00, 107.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribosome biogenesis protein 15 / Nucleolar protein 15


Mass: 13048.288 Da / Num. of mol.: 4 / Fragment: residues 81-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NOP15, YNL110C, N1954 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P53927
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.06 Å / Num. obs: 33029 / % possible obs: 94.57 % / Redundancy: 3.5 % / Net I/σ(I): 8.53

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.02
RfactorNum. reflection% reflection
Rfree0.2356 2000 6.06 %
Rwork0.1915 --
obs0.1942 33014 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 62 243 3607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113439
X-RAY DIFFRACTIONf_angle_d1.2964602
X-RAY DIFFRACTIONf_dihedral_angle_d14.5621328
X-RAY DIFFRACTIONf_chiral_restr0.057470
X-RAY DIFFRACTIONf_plane_restr0.006573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.326890.24891370X-RAY DIFFRACTION58
2.05-2.10540.27341220.21851896X-RAY DIFFRACTION82
2.1054-2.16740.27841380.21052142X-RAY DIFFRACTION92
2.1674-2.23730.23231440.19912231X-RAY DIFFRACTION96
2.2373-2.31730.26061500.19752330X-RAY DIFFRACTION99
2.3173-2.410.25581480.19862301X-RAY DIFFRACTION99
2.41-2.51970.24461510.20772350X-RAY DIFFRACTION100
2.5197-2.65260.27251510.20852334X-RAY DIFFRACTION100
2.6526-2.81870.29461500.21642331X-RAY DIFFRACTION100
2.8187-3.03630.27141500.19692326X-RAY DIFFRACTION100
3.0363-3.34180.23231520.19852359X-RAY DIFFRACTION100
3.3418-3.82510.19721510.17942341X-RAY DIFFRACTION100
3.8251-4.81840.17841510.15352350X-RAY DIFFRACTION100
4.8184-45.06710.24311530.19632353X-RAY DIFFRACTION99

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