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- PDB-2vnu: Crystal structure of Sc Rrp44 -

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Basic information

Entry
Database: PDB / ID: 2vnu
TitleCrystal structure of Sc Rrp44
Components
  • 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP)-3'
  • EXOSOME COMPLEX EXONUCLEASE RRP44
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / RNA DEGRADATION / RNA-BINDING / RNA 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 mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / exosome (RNase complex) ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / exosome (RNase complex) / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA catabolic process / nuclear mRNA surveillance / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nonfunctional rRNA decay / 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 / nucleus
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #690 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / Exosome complex exonuclease RRP44, S1 domain / S1 domain / 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) / Ribonuclease II/R, conserved site ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #690 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / Exosome complex exonuclease RRP44, S1 domain / S1 domain / 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) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / Exosome complex exonuclease DIS3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLorentzen, E. / Basquin, J. / Conti, E.
CitationJournal: Mol.Cell / Year: 2008
Title: Structure of the Active Subunit of the Yeast Exosome Core, Rrp44: Diverse Modes of Substrate Recruitment in the Rnase II Nuclease Family
Authors: Lorentzen, E. / Basquin, J. / Tomecki, R. / Dziembowski, A. / Conti, E.
History
DepositionFeb 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP)-3'
D: EXOSOME COMPLEX EXONUCLEASE RRP44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5735
Polymers90,2872
Non-polymers2863
Water8,107450
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-1.8 kcal/mol
Surface area37660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.350, 87.250, 136.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain / Protein , 2 types, 2 molecules BD

#1: RNA chain 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP)-3'


Mass: 3247.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Protein EXOSOME COMPLEX EXONUCLEASE RRP44 / RIBOSOMAL RNA-PROCESSING PROTEIN 44 / PROTEIN DIS3 / RRP44


Mass: 87039.930 Da / Num. of mol.: 1 / Fragment: RESIDUES 242-1001 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08162

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Non-polymers , 4 types, 453 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN D, ASP 551 TO ASN
Has protein modificationY
Sequence detailsD551N MUTATION

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6 / Details: 15% PEG 400, 50 MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 37745 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.8 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→29.06 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.874 / SU B: 15.863 / SU ML: 0.212 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1168 3 %RANDOM
Rwork0.217 ---
obs0.219 37745 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 199 18 450 6047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4922.0087906
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02323.927247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34615922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.751538
X-RAY DIFFRACTIONr_chiral_restr0.1180.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024308
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22726
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23890
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2410
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.56233493
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0244.55638
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8432378
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.35962261
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 84
Rwork0.273 2702
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)
12.9270.64330.1993.5645-2.11037.47040.04670.09160.0374-0.0473-0.0994-0.1408-0.18260.50910.0528-0.09090.0365-0.0838-0.14250.0165-0.093641.55776.06717.695
24.96943.0328-0.61888.7355-0.73684.699-0.0586-0.1191-0.30050.1762-0.1430.48550.3068-0.27040.2017-0.1134-0.0142-0.0125-0.0529-0.0217-0.052623.09661.66523.271
31.5165-0.2297-0.0811.03960.33891.11830.05050.0363-0.09560.0008-0.02240.1395-0.0445-0.075-0.0282-0.1419-0.00360.028-0.1690.0035-0.20956.77440.62216.986
43.3288-1.9739-0.70565.57311.0162.9396-0.1859-0.2396-0.090.34480.14490.64330.0907-0.30660.0409-0.1310.02080.008-0.02030.052-0.124946.74565.42945.072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D252 - 398
2X-RAY DIFFRACTION2D399 - 473
3X-RAY DIFFRACTION3D474 - 910
4X-RAY DIFFRACTION4D911 - 999

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