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- PDB-2wp8: yeast rrp44 nuclease -

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Basic information

Entry
Database: PDB / ID: 2wp8
Titleyeast rrp44 nuclease
Components
  • EXOSOME COMPLEX COMPONENT RRP45
  • EXOSOME COMPLEX COMPONENT SKI6
  • EXOSOME COMPLEX EXONUCLEASE DIS3
KeywordsHYDROLASE / EXOSOME / NUCLEUS / NUCLEASE / RNA-BINDING / EXONUCLEASE / RNA BINDING / MITOCHONDRION / RRNA PROCESSING
Function / homology
Function and homology information


Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / : / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / nuclear mRNA surveillance / rRNA catabolic process / nonfunctional rRNA decay / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / RNA endonuclease activity / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / endonuclease activity / tRNA binding / nucleolus / mitochondrion / RNA binding / nucleus
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / Exosome complex exonuclease RRP44, S1 domain / S1 domain / Exosome complex component RRP45 / PIN domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / GHMP Kinase, N-terminal domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / Exosome complex exonuclease RRP44, S1 domain / S1 domain / Exosome complex component RRP45 / PIN domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / GHMP Kinase, N-terminal domain / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / 5'-nuclease / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Exosome complex component SKI6 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBasquin, J. / Bonneau, F. / Ebert, J. / Lorentzen, E. / Conti, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation.
Authors: Bonneau, F. / Basquin, J. / Ebert, J. / Lorentzen, E. / Conti, E.
History
DepositionAug 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXOSOME COMPLEX COMPONENT RRP45
B: EXOSOME COMPLEX COMPONENT SKI6
J: EXOSOME COMPLEX EXONUCLEASE DIS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,9715
Polymers172,8433
Non-polymers1282
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-33.9 kcal/mol
Surface area59520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.900, 125.680, 139.400
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 EXOSOME COMPLEX COMPONENT RRP45


Mass: 34001.859 Da / Num. of mol.: 1
Fragment: EXOSOME NON-CATALYTIC CORE COMPONENT RRP45, RIBOSOMAL RNA-PROCESSING PROTEIN 45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q05636, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein EXOSOME COMPLEX COMPONENT SKI6 / EXOSOME NON-CATALYTIC CORE COMPONENT RRP41 / SUPERKILLER PROTEIN 6 / RIBOSOMAL RNA-PROCESSING ...EXOSOME NON-CATALYTIC CORE COMPONENT RRP41 / SUPERKILLER PROTEIN 6 / RIBOSOMAL RNA-PROCESSING PROTEIN 41 / EXTRACELLULAR MUTANT PROTEIN 20


Mass: 27612.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PETMCN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P46948, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Protein EXOSOME COMPLEX EXONUCLEASE DIS3 / EXOSOME CORE COMPLEX CATALYTIC SUBUNIT RRP44 / CHROMOSOME DISJUNCTION PROTEIN 3 / RIBOSOMAL RNA- ...EXOSOME CORE COMPLEX CATALYTIC SUBUNIT RRP44 / CHROMOSOME DISJUNCTION PROTEIN 3 / RIBOSOMAL RNA-PROCESSING PROTEIN 44


Mass: 111228.594 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-1001 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PETMCN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Compound detailsENGINEERED RESIDUE IN CHAIN J, ASP 551 TO ASN

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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: 2.86 Å3/Da / Density % sol: 57.03 % / Description: NONE
Crystal growpH: 8
Details: 7.5 % (W/V) OF PEG 20.000, 50 MM TRIS PH 8.0 AND 10% (W/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 39670 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 21
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2NN6, 2VNU

2nn6

2vnu


Resolution: 3→19.99 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.848 / SU B: 40.476 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27291 1185 3 %RANDOM
Rwork0.20698 ---
obs0.20899 38325 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.452 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10809 0 7 0 10816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210987
X-RAY DIFFRACTIONr_bond_other_d0.0010.027310
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.96514916
X-RAY DIFFRACTIONr_angle_other_deg0.936317869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38851384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75824.286490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.127151857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.871574
X-RAY DIFFRACTIONr_chiral_restr0.0820.21740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022143
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4861.56963
X-RAY DIFFRACTIONr_mcbond_other0.0741.52788
X-RAY DIFFRACTIONr_mcangle_it0.938211237
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.36534024
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3644.53679
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 84 -
Rwork0.272 2740 -
obs--100 %
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)
13.97171.14921.31243.2194-0.30823.16970.0144-0.5348-0.13080.4555-0.0746-0.2621-0.1910.22290.06030.1233-0.0085-0.04630.1680.01720.0824-30.984-59.77377.108
21.5630.66810.24170.89460.14340.54090.004-0.00070.1352-0.0014-0.00710.0393-0.09210.03890.00320.1-0.0151-0.00950.1339-0.0180.0814-57.881-52.24931.758
36.2305-0.1968-0.66811.28940.15931.0883-0.0440.0682-0.1631-0.0503-0.01530.3192-0.0904-0.12960.05940.01040.0109-0.01220.0155-0.00610.0812-67.595-60.34160.608
400000000000000-00.23310.17140.11090.1260.0810.1818-11.438-26.79458.608
52.27730.78550.18882.65050.36030.97660.1064-0.1545-0.0450.3233-0.0329-0.19590.15150.0159-0.07360.0539-0.0039-0.02940.01380.00020.017-25.355-30.01753.299
61.01420.1094-0.21460.92290.28171.61420.01360.03760.0085-0.05930.063-0.2274-0.05930.1089-0.07650.0931-0.02120.02690.0644-0.02590.1501-9.591-30.88518.257
73.41340.2781.20372.199-0.23616.33220.0652-0.3193-0.37840.2456-0.0288-0.11260.80460.308-0.03630.27840.1172-0.08590.22010.02250.32-3.618-46.08953.271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1J37 - 198
2X-RAY DIFFRACTION2A7 - 303
3X-RAY DIFFRACTION3B4 - 238
4X-RAY DIFFRACTION4B1240
5X-RAY DIFFRACTION5J253 - 475
6X-RAY DIFFRACTION6J476 - 910
7X-RAY DIFFRACTION7J911 - 1001

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