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- PDB-5wwm: Crystal structure of the TPR domain of Rrp5 -

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Basic information

Entry
Database: PDB / ID: 5wwm
TitleCrystal structure of the TPR domain of Rrp5
ComponentsrRNA biogenesis protein RRP5
KeywordsRNA BINDING PROTEIN / component of 90S preribosome
Function / homology
Function and homology information


box H/ACA snoRNA binding / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome assembly / rRNA primary transcript binding / poly(U) RNA binding / U3 snoRNA binding / snoRNA binding ...box H/ACA snoRNA binding / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome assembly / rRNA primary transcript binding / poly(U) RNA binding / U3 snoRNA binding / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / 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 / rRNA processing / mRNA binding / nucleolus / RNA binding / nucleoplasm
Similarity search - Function
rRNA biogenesis protein Rrp5 / : / : / Suppressor of forked / Suppressor of forked protein (Suf) / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain ...rRNA biogenesis protein Rrp5 / : / : / Suppressor of forked / Suppressor of forked protein (Suf) / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
rRNA biogenesis protein RRP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.809 Å
AuthorsYe, K. / Chen, X.
CitationJournal: Elife / Year: 2017
Title: Correction: Molecular architecture of the 90S small subunit pre-ribosome
Authors: Sun, Q. / Zhu, X. / Qi, J. / An, W. / Lan, P. / Tan, D. / Chen, R. / Wang, B. / Zheng, S. / Zhang, C. / Chen, X. / Zhang, W. / Chen, J. / Dong, M.Q. / Ye, K.
History
DepositionJan 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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
A: rRNA biogenesis protein RRP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7644
Polymers38,4761
Non-polymers2883
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.526, 114.526, 70.933
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein rRNA biogenesis protein RRP5 / Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA- ...Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA-associated protein RRP5


Mass: 38476.246 Da / Num. of mol.: 1 / Fragment: UNP residues 1399-1729
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP5, FMI1, YMR229C, YM9959.11C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05022
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.49 Å3/Da / Density % sol: 64.76 % / Mosaicity: 0.701 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium citrate, pH 5.6

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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: Jul 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 13319 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.125 / Net I/av σ(I): 38.276 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.85140.6261100
2.85-2.914.10.5181100
2.9-2.9614.10.451100
2.96-3.0214.10.391100
3.02-3.08140.3131100
3.08-3.1514.20.2811100
3.15-3.23140.2291100
3.23-3.3214.20.2031100
3.32-3.41140.1681100
3.41-3.52140.1521100
3.52-3.65140.1361100
3.65-3.7913.70.1231100
3.79-3.9713.70.1181100
3.97-4.1713.50.1081100
4.17-4.4313.30.1071100
4.43-4.7712.90.1051100
4.77-5.2412.90.1031100
5.24-5.9812.70.0951100
5.98-7.4712.40.0831100
7.47-2011.90.06199.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
PHENIXphasing
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.809→19.999 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.56
RfactorNum. reflection% reflection
Rfree0.258 657 4.94 %
Rwork0.2046 --
obs0.2071 13300 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.38 Å2 / Biso mean: 62.7952 Å2 / Biso min: 22.75 Å2
Refinement stepCycle: final / Resolution: 2.809→19.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 15 6 2249
Biso mean--85.59 46.26 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082283
X-RAY DIFFRACTIONf_angle_d0.9933072
X-RAY DIFFRACTIONf_chiral_restr0.055332
X-RAY DIFFRACTIONf_plane_restr0.005387
X-RAY DIFFRACTIONf_dihedral_angle_d19.0191373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8087-3.02490.27091490.23072424257399
3.0249-3.32810.31831140.234825342648100
3.3281-3.80680.24861200.201925322652100
3.8068-4.78530.25071380.191425412679100
4.7853-19.99920.2451360.198626122748100

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