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- PDB-3fqd: Crystal Structure of the S. pombe Rat1-Rai1 Complex -

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Basic information

Entry
Database: PDB / ID: 3fqd
TitleCrystal Structure of the S. pombe Rat1-Rai1 Complex
Components
  • 5'-3' exoribonuclease 2
  • Protein din1
KeywordsHYDROLASE/PROTEIN BINDING / Protein-Protein Complex / Exonuclease / Hydrolase / mRNA processing / Nuclease / Nucleus / rRNA processing / Transcription / Transcription regulation / Transcription termination / Phosphoprotein / HYDROLASE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


5'-hydroxyl dinucleotide hydrolase activity / : / positive regulation of chromosome segregation / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / phosphodiesterase decapping endonuclease activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / 5'-3' RNA exonuclease activity / nucleic acid metabolic process ...5'-hydroxyl dinucleotide hydrolase activity / : / positive regulation of chromosome segregation / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / phosphodiesterase decapping endonuclease activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / 5'-3' RNA exonuclease activity / nucleic acid metabolic process / nuclear mRNA surveillance / nuclear-transcribed mRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / DNA-templated transcription termination / mRNA processing / GDP binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / RNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / RAI1-like / RAI1 like PD-(D/E)XK nuclease / RAI1-like family
Similarity search - Domain/homology
Decapping nuclease din1 / 5'-3' exoribonuclease 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsXiang, S. / Tong, L.
CitationJournal: Nature / Year: 2009
Title: Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1.
Authors: Xiang, S. / Cooper-Morgan, A. / Jiao, X. / Kiledjian, M. / Manley, J.L. / Tong, L.
History
DepositionJan 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-3' exoribonuclease 2
B: Protein din1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7024
Polymers144,5862
Non-polymers1162
Water11,674648
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.690, 190.869, 84.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 5'-3' exoribonuclease 2 / Protein dhp1


Mass: 103270.031 Da / Num. of mol.: 1 / Fragment: Rat1, residue 1-885
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: dhp1, Rat1, SPAC26A3.12c / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: P40848, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein Protein din1 / Dhp1-interacting protein 1


Mass: 41315.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: din1, Rai1, SPAC19D5.06c / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O13836
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.3 M sodium malonate (pH 5.0), 10 mM DTT and 14 % (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9806 Å
DetectorType: Mar m-165 CCD / Detector: CCD / Date: Feb 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9806 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 77326 / % possible obs: 92.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Χ2: 1.088 / Net I/σ(I): 17.502
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.282.70.35649251.126159.9
2.28-2.372.90.36165991.173179.6
2.37-2.483.40.34376541.136192.8
2.48-2.613.90.28880811.134197.6
2.61-2.774.30.22481881.105198.6
2.77-2.994.40.1681981.084198.8
2.99-3.294.50.09882851.056199
3.29-3.764.50.06282881.07199.2
3.76-4.734.50.04484131.036199.4
4.73-304.30.0486951.067199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0003refinement
PDB_EXTRACT3.006data extraction
SnBphasing
RefinementResolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.018 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3837 5.1 %RANDOM
Rwork0.218 ---
obs0.22 75616 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 163.38 Å2 / Biso mean: 44.537 Å2 / Biso min: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2---2.41 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8271 0 7 648 8926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228492
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.95211516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2651008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53624.015411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.065151489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0121558
X-RAY DIFFRACTIONr_chiral_restr0.0710.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026492
X-RAY DIFFRACTIONr_nbd_refined0.1860.23971
X-RAY DIFFRACTIONr_nbtor_refined0.3010.25686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2615
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.221
X-RAY DIFFRACTIONr_mcbond_it0.5491.55282
X-RAY DIFFRACTIONr_mcangle_it0.77628302
X-RAY DIFFRACTIONr_scbond_it1.00633695
X-RAY DIFFRACTIONr_scangle_it1.554.53214
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 194 -
Rwork0.287 3617 -
all-3811 -
obs--65.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8204-0.40280.01042.50840.5550.68580.09460.09650.1401-0.5356-0.0572-0.1042-0.2429-0.0469-0.03750.01540.05710.0271-0.09160.0063-0.139322.768964.828919.9992
20.7584-0.03360.19743.17750.2020.45690.0442-0.0103-0.0223-0.11910.00520.12310.0141-0.041-0.0494-0.13040.0127-0.0104-0.10950.0074-0.171535.031213.76922.4686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 878
2X-RAY DIFFRACTION2B1 - 352

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