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- PDB-9cy7: Structure of S.pombe Dis3L2 in complex with oligoU RNA substrate -

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Basic information

Entry
Database: PDB / ID: 9cy7
TitleStructure of S.pombe Dis3L2 in complex with oligoU RNA substrate
Components
  • DIS3-like exonuclease 2
  • U13 RNA
KeywordsHYDROLASE / Dis3L2 / oligoU RNA
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / P-body / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / DIS3-like exonuclease 2-like, C-terminal / DIS3-like exonuclease 2 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain ...: / DIS3-like exonuclease 2-like, C-terminal / DIS3-like exonuclease 2 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / DIS3-like exonuclease 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Schizosaccharomyces pombe 927 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsGarg, A. / Joshua-Tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Structure of S.pombe Dis3L2 in complex with oligoU RNA substrate
Authors: Garg, A. / Joshua-Tor, L.
History
DepositionAug 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIS3-like exonuclease 2
B: DIS3-like exonuclease 2
C: U13 RNA
D: U13 RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,6936
Polymers180,6444
Non-polymers492
Water181
1
A: DIS3-like exonuclease 2
C: U13 RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3463
Polymers90,3222
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-38 kcal/mol
Surface area33400 Å2
MethodPISA
2
B: DIS3-like exonuclease 2
D: U13 RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3463
Polymers90,3222
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-48 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.838, 122.838, 296.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DIS3-like exonuclease 2


Mass: 86386.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: dis32, dis3l2, SPAC2C4.07c / Production host: Escherichia coli (E. coli)
References: UniProt: O14040, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: RNA chain U13 RNA


Mass: 3935.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe 927 (yeast)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 4000, 100 mM HEPES pH 7.5, and 100 mM Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 3.51→29.79 Å / Num. obs: 29105 / % possible obs: 99.6 % / Redundancy: 22 % / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Net I/σ(I): 17.67
Reflection shellResolution: 3.51→3.64 Å / Num. unique obs: 2820 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487:0000)refinement
autoPROCdata processing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→29.79 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3103 1996 6.89 %
Rwork0.2818 --
obs0.2838 28981 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.52→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11072 480 2 1 11555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311827
X-RAY DIFFRACTIONf_angle_d0.63916087
X-RAY DIFFRACTIONf_dihedral_angle_d12.571790
X-RAY DIFFRACTIONf_chiral_restr0.0431829
X-RAY DIFFRACTIONf_plane_restr0.0041988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.52-3.60.35961370.35711837X-RAY DIFFRACTION98
3.6-3.70.4081370.35371894X-RAY DIFFRACTION99
3.7-3.810.39841410.34221881X-RAY DIFFRACTION100
3.81-3.930.34581380.33331885X-RAY DIFFRACTION100
3.93-4.070.37091410.3471896X-RAY DIFFRACTION100
4.07-4.240.42141420.34071923X-RAY DIFFRACTION100
4.24-4.430.35751400.30811891X-RAY DIFFRACTION100
4.43-4.660.35851430.30891916X-RAY DIFFRACTION100
4.66-4.950.29781420.28771929X-RAY DIFFRACTION100
4.95-5.330.29771440.27921938X-RAY DIFFRACTION100
5.33-5.860.31721430.31341939X-RAY DIFFRACTION100
5.86-6.70.35651450.31371955X-RAY DIFFRACTION100
6.7-8.410.29471480.26851992X-RAY DIFFRACTION100
8.42-29.790.21821550.19882109X-RAY DIFFRACTION100

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