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- PDB-5svd: Nop9, a new PUF-like protein, prevents premature pre-rRNA cleavag... -

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Basic information

Entry
Database: PDB / ID: 5svd
TitleNop9, a new PUF-like protein, prevents premature pre-rRNA cleavage to correctly process mature 18S rRNA
ComponentsNucleolar protein 9Nucleolus
KeywordsRNA BINDING PROTEIN / Nop9 / PUF-like proteins / ITS1 ribosome biogenesis / RNA-binding protein
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 / 90S preribosome / 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) / 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 / 90S preribosome / 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) / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, J. / Qiu, C. / Hall, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES050165-18 United States
CitationJournal: Nat Commun / Year: 2016
Title: Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA.
Authors: Zhang, J. / McCann, K.L. / Qiu, C. / Gonzalez, L.E. / Baserga, S.J. / Hall, T.M.
History
DepositionAug 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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
A: Nucleolar protein 9
B: Nucleolar protein 9


Theoretical massNumber of molelcules
Total (without water)139,8952
Polymers139,8952
Non-polymers00
Water6,792377
1
A: Nucleolar protein 9


Theoretical massNumber of molelcules
Total (without water)69,9471
Polymers69,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleolar protein 9


Theoretical massNumber of molelcules
Total (without water)69,9471
Polymers69,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.501, 110.466, 114.846
Angle α, β, γ (deg.)90.00, 92.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 69947.492 Da / Num. of mol.: 2 / Fragment: residues 46-645 / Mutation: A430T
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 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P47077
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18% (w/v) PEG 3350, 0.2 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 96076 / % possible obs: 97.5 % / Redundancy: 7 % / Net I/σ(I): 12.5
Reflection shellHighest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Coot0.8.1model building
PHENIX1.9_1692phasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.1→32.022 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2212 1985 2.1 %
Rwork0.1848 --
obs0.1855 94387 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→32.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8794 0 0 377 9171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098975
X-RAY DIFFRACTIONf_angle_d1.11212105
X-RAY DIFFRACTIONf_dihedral_angle_d13.0063376
X-RAY DIFFRACTIONf_chiral_restr0.0461387
X-RAY DIFFRACTIONf_plane_restr0.0061511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0972-2.14970.29381130.26395272X-RAY DIFFRACTION77
2.1497-2.20780.26561370.24346213X-RAY DIFFRACTION90
2.2078-2.27270.2551430.23186480X-RAY DIFFRACTION95
2.2727-2.34610.25841270.2166621X-RAY DIFFRACTION96
2.3461-2.42990.27031560.21556603X-RAY DIFFRACTION97
2.4299-2.52710.28021410.22086655X-RAY DIFFRACTION97
2.5271-2.64210.2691470.21536736X-RAY DIFFRACTION98
2.6421-2.78130.27531410.22226766X-RAY DIFFRACTION98
2.7813-2.95550.24441450.21856817X-RAY DIFFRACTION99
2.9555-3.18350.23231510.21586815X-RAY DIFFRACTION99
3.1835-3.50350.2441420.20036836X-RAY DIFFRACTION99
3.5035-4.00960.20091500.16826873X-RAY DIFFRACTION100
4.0096-5.04850.16631470.1436910X-RAY DIFFRACTION100
5.0485-32.02590.19951450.15456805X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 14.8414 Å / Origin y: -5.4205 Å / Origin z: 29.5817 Å
111213212223313233
T0.3716 Å20.025 Å20.0614 Å2-0.3681 Å2-0.0181 Å2--0.3879 Å2
L-0.1164 °20.0789 °20.2146 °2-0.0127 °20.0101 °2--0.0327 °2
S-0.0402 Å °0.0247 Å °0.0468 Å °-0.04 Å °0.0245 Å °0.0098 Å °-0.1067 Å °-0.0332 Å °0.013 Å °
Refinement TLS groupSelection details: all

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