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- PDB-5i2t: Domain characterization of the WD protein Pwp2 and their relevanc... -

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Basic information

Entry
Database: PDB / ID: 5i2t
TitleDomain characterization of the WD protein Pwp2 and their relevance in ribosome biogenesis
ComponentsPeriodic tryptophan protein 2
KeywordsBIOSYNTHETIC PROTEIN / ribosome biogenesis / WD
Function / homology
Function and homology information


Pwp2p-containing subcomplex of 90S preribosome / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / establishment of cell polarity / 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 from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA ...Pwp2p-containing subcomplex of 90S preribosome / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / establishment of cell polarity / 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 from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / ribosomal small subunit assembly / mRNA binding / nucleolus / nucleoplasm / cytoplasm
Similarity search - Function
Periodic tryptophan protein 2 / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...Periodic tryptophan protein 2 / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Periodic tryptophan protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.543 Å
AuthorsFribourg, S. / Boissier, F.
CitationJournal: Sci Rep / Year: 2017
Title: Pwp2 mediates UTP-B assembly via two structurally independent domains.
Authors: Boissier, F. / Schmidt, C.M. / Linnemann, J. / Fribourg, S. / Perez-Fernandez, J.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all
Revision 1.2Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Periodic tryptophan protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4182
Polymers83,3221
Non-polymers961
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.830, 76.040, 191.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Periodic tryptophan protein 2 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1


Mass: 83321.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PWP2, UTP1, YCR057C, YCR55C/YCR57C/YCR58C / Production host: Escherichia coli (E. coli) / References: UniProt: P25635
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 5 % polyethylene glycol 6000, 0.1 M Magnesium Sulphate

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.54→47.398 Å / Num. obs: 34863 / % possible obs: 99.8 % / Redundancy: 8.74 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0187 / Rpim(I) all: 0.046 / Net I/σ(I): 12
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4990 / CC1/2: 0.536 / Rpim(I) all: 0.651 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBI

2pbi


Resolution: 2.543→47.398 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.83
RfactorNum. reflection% reflection
Rfree0.2521 1734 5 %
Rwork0.2134 --
obs0.2153 34668 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.543→47.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 5 44 4839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114903
X-RAY DIFFRACTIONf_angle_d1.3746640
X-RAY DIFFRACTIONf_dihedral_angle_d16.5861728
X-RAY DIFFRACTIONf_chiral_restr0.078738
X-RAY DIFFRACTIONf_plane_restr0.007850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5429-2.61770.42991380.42222617X-RAY DIFFRACTION97
2.6177-2.70220.40191410.38832681X-RAY DIFFRACTION100
2.7022-2.79880.3631430.35032719X-RAY DIFFRACTION100
2.7988-2.91080.35241420.32022701X-RAY DIFFRACTION100
2.9108-3.04330.33971440.32432738X-RAY DIFFRACTION100
3.0433-3.20370.33891430.27592719X-RAY DIFFRACTION100
3.2037-3.40440.30711440.23942734X-RAY DIFFRACTION100
3.4044-3.66710.2321440.21732744X-RAY DIFFRACTION100
3.6671-4.0360.23921460.19352763X-RAY DIFFRACTION100
4.036-4.61960.18131460.15212769X-RAY DIFFRACTION100
4.6196-5.81850.1931480.15652816X-RAY DIFFRACTION100
5.8185-47.40590.23621550.18362933X-RAY DIFFRACTION100

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