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- PDB-6wpi: Crystal structure of Nop9 in complex with ITS1 RNA -

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Basic information

Entry
Database: PDB / ID: 6wpi
TitleCrystal structure of Nop9 in complex with ITS1 RNA
Components
  • Nucleolar protein 9
  • RNA (47-MER)
KeywordsRNA BINDING PROTEIN/RNA / Nop9 / PUF protein / ribosome biogenesis / RNA BINDING PROTEIN / 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
3,3',3''-phosphanetriyltripropanoic acid / RNA / RNA (> 10) / Nucleolar protein 9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.02 Å
AuthorsZhang, J. / Qiu, C. / Hall, T.M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA5016 United States
CitationJournal: Rna / Year: 2020
Title: Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA.
Authors: Zhang, J. / Teramoto, T. / Qiu, C. / Wine, R.N. / Gonzalez, L.E. / Baserga, S.J. / Tanaka Hall, T.M.
History
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleolar protein 9
B: RNA (47-MER)
C: RNA (47-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3865
Polymers99,0433
Non-polymers3422
Water00
1
A: Nucleolar protein 9
B: RNA (47-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2644
Polymers83,9212
Non-polymers3422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (47-MER)


Theoretical massNumber of molelcules
Total (without water)15,1221
Polymers15,1221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.925, 119.540, 142.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 68799.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NOP9, YJL010C, J1357 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47077
#2: RNA chain RNA (47-MER)


Mass: 15121.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast)
#3: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN

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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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 18% (w/v) PEG 3350, 0.2 M ammonium citrate, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 24604 / % possible obs: 99.8 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Χ2: 0.911 / Net I/σ(I): 8.2 / Num. measured all: 354389
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3-3.05150.96711850.9170.2580.586100
3.05-3.1114.90.69112210.9580.1840.6181000.716
3.11-3.1714.90.5712020.9670.1520.631000.59
3.17-3.2314.90.47712250.9760.1270.6351000.494
3.23-3.3150.39512060.980.1050.6561000.409
3.3-3.3814.90.29712260.9890.0790.681000.308
3.38-3.4614.90.23412030.9910.0620.7311000.242
3.46-3.5614.90.18212130.9950.0490.8071000.188
3.56-3.6614.80.15212040.9960.0410.8551000.158
3.66-3.7814.80.12812340.9970.0340.9581000.132
3.78-3.9114.80.10612050.9980.0291.0171000.11
3.91-4.0714.60.09212390.9980.0251.1461000.095
4.07-4.2614.60.08112160.9980.0221.21000.084
4.26-4.4814.50.07412430.9980.021.1961000.076
4.48-4.7614.40.06812460.9990.0181.1051000.07
4.76-5.1314.30.06512290.9990.0181.1511000.067
5.13-5.6414.20.0612440.9990.0161.13799.90.062
5.64-6.4613.90.05612590.9990.0161.1581000.059
6.46-8.1313.20.04612760.9990.0131.021000.048
8.13-5010.70.03713280.9990.012197.10.039

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5svd

5svd


Resolution: 3.02→34.75 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 1996 8.15 %
Rwork0.1953 22506 -
obs0.1984 24502 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.57 Å2 / Biso mean: 106.7599 Å2 / Biso min: 58.66 Å2
Refinement stepCycle: final / Resolution: 3.02→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 1417 22 0 5929
Biso mean--108.57 --
Num. residues----615
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.02-3.090.32891270.28061438156590
3.09-3.180.31781420.280315871729100
3.18-3.270.31541430.277216091752100
3.27-3.380.31821410.267215851726100
3.38-3.50.32051400.241315911731100
3.5-3.640.27321440.23116191763100
3.64-3.80.28921410.235215951736100
3.8-40.27831440.218316191763100
4-4.250.27841420.184716141756100
4.25-4.580.22831440.177316091753100
4.58-5.040.22791450.181416371782100
5.04-5.770.21691440.193116351779100
5.77-7.250.22631480.199216671815100
7.26-34.750.16561510.15651701185297

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