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- PDB-5wty: Structure of Nop9 RNA complex -

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Basic information

Entry
Database: PDB / ID: 5wty
TitleStructure of Nop9 RNA complex
Components
  • Nucleolar protein 9
  • RNA (5'-R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / Pumilio repeat-containing protein / RNA-binding protein / RNP / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / ribosomal small subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA / small-subunit processome / mRNA binding / nucleolus ...endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / ribosomal small subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA / small-subunit processome / mRNA binding / nucleolus / RNA binding / nucleus
Similarity search - Function
Nucleolar protein 9 / Pumilio RNA-binding repeat / Pumilio-like repeats / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleolar protein 9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.785 Å
AuthorsYe, K. / Wang, B.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Nop9 binds the central pseudoknot region of 18S rRNA
Authors: Wang, B. / Ye, K.
History
DepositionDec 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Mar 20, 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: Nucleolar protein 9
A: Nucleolar protein 9
C: RNA (5'-R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')
D: RNA (5'-R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)148,3384
Polymers148,3384
Non-polymers00
Water1,874104
1
B: Nucleolar protein 9
D: RNA (5'-R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)74,1692
Polymers74,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint1 kcal/mol
Surface area27230 Å2
MethodPISA
2
A: Nucleolar protein 9
C: RNA (5'-R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)74,1692
Polymers74,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint4 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.503, 102.744, 114.708
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleolar protein 9 / Pumilio domain-containing protein NOP9


Mass: 68246.469 Da / Num. of mol.: 2 / Fragment: UNP residues 53-634
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NOP9 / Production host: Escherichia coli (E. coli) / References: UniProt: P47077
#2: RNA chain RNA (5'-R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')


Mass: 5922.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate tribasic dihydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.785→50 Å / Num. obs: 39356 / Redundancy: 5.3 % / Net I/σ(I): 18.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.785→19.959 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.55
RfactorNum. reflection% reflection
Rfree0.237 1974 5.02 %
Rwork0.1765 --
obs0.1796 39356 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.785→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8934 482 0 104 9520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099637
X-RAY DIFFRACTIONf_angle_d1.19913103
X-RAY DIFFRACTIONf_dihedral_angle_d19.9383701
X-RAY DIFFRACTIONf_chiral_restr0.0481510
X-RAY DIFFRACTIONf_plane_restr0.0051559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7853-2.85470.35981130.26922142X-RAY DIFFRACTION80
2.8547-2.93170.35391320.24922634X-RAY DIFFRACTION97
2.9317-3.01770.31841550.23182707X-RAY DIFFRACTION100
3.0177-3.11470.28841440.21542686X-RAY DIFFRACTION100
3.1147-3.22560.31131620.2082694X-RAY DIFFRACTION100
3.2256-3.35420.2631460.20172713X-RAY DIFFRACTION100
3.3542-3.50610.2611390.18392702X-RAY DIFFRACTION100
3.5061-3.68980.24461190.17222749X-RAY DIFFRACTION100
3.6898-3.91940.21681520.16432694X-RAY DIFFRACTION100
3.9194-4.21940.20171360.15592735X-RAY DIFFRACTION100
4.2194-4.63910.20611310.13842756X-RAY DIFFRACTION100
4.6391-5.29940.20651360.15432717X-RAY DIFFRACTION100
5.2994-6.63570.24211510.1892734X-RAY DIFFRACTION100
6.6357-19.95980.16461580.14282719X-RAY DIFFRACTION98

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