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- PDB-1sq9: Structure of Ski8p, a WD repeat protein involved in mRNA degradat... -

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Basic information

Entry
Database: PDB / ID: 1sq9
TitleStructure of Ski8p, a WD repeat protein involved in mRNA degradation and meiotic recombination
ComponentsAntiviral protein SKI8Antiviral drug
KeywordsANTIVIRAL PROTEIN / RECOMBINATION / WD repeat / beta-transducin repeat / WD40 repeat / beta propeller
Function / homology
Function and homology information


Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / reciprocal meiotic recombination / nuclear chromosome / mRNA catabolic process / protein-containing complex assembly ...Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / reciprocal meiotic recombination / nuclear chromosome / mRNA catabolic process / protein-containing complex assembly / defense response to virus / nucleus
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Antiviral protein SKI8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.9 Å
AuthorsMadrona, A.Y. / Wilson, D.K.
CitationJournal: Protein Sci. / Year: 2004
Title: The structure of Ski8p, a protein regulating mRNA degradation: Implications for WD protein structure.
Authors: Madrona, A.Y. / Wilson, D.K.
History
DepositionMar 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antiviral protein SKI8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4763
Polymers44,2841
Non-polymers1922
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.54, 67.64, 80.31
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Antiviral protein SKI8 / Antiviral drug


Mass: 44283.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI8, REC103, YGL213C / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: Q02793
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ammonium sulfate, cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 0.9791, 0.9184, 0.9793
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 6, 2002 / Details: Yale mirrors
RadiationMonochromator: Yale mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.91841
30.97931
ReflectionResolution: 1.9→100 Å / Num. all: 28833 / Num. obs: 28833 / % possible obs: 100 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 32
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameClassification
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 1438 random
Rwork0.191 --
obs0.191 28769 -
all-28795 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 10 230 3211
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7

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