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- PDB-2hbk: Structure of the yeast nuclear exosome component, Rrp6p, reveals ... -

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Basic information

Entry
Database: PDB / ID: 2hbk
TitleStructure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn
ComponentsExosome complex exonuclease RRP6
KeywordsHYDROLASE / GENE REGULATION / exosome / RNA metabolism / RNA surveillance / RNA processing
Function / homology
Function and homology information


nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process ...nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / 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) / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone mRNA catabolic process / nuclear mRNA surveillance / rRNA primary transcript binding / RNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / single-stranded RNA binding / nucleotide binding / nucleolus / nucleus
Similarity search - Function
: / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / PMC2NT (NUC016) domain / HRDC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily ...: / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / PMC2NT (NUC016) domain / HRDC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Exosome complex exonuclease RRP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsMidtgaard, S.F. / Assenholt, J. / Jonstrup, A.T. / Van, L.B. / Jensen, T.H. / Brodersen, D.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain.
Authors: Midtgaard, S.F. / Assenholt, J. / Jonstrup, A.T. / Van, L.B. / Jensen, T.H. / Brodersen, D.E.
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exosome complex exonuclease RRP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7853
Polymers47,6751
Non-polymers1102
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.680, 110.680, 79.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is the monomer present in the asymmetric unit.

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Components

#1: Protein Exosome complex exonuclease RRP6 / Ribosomal RNA- processing protein 6


Mass: 47675.125 Da / Num. of mol.: 1 / Fragment: Rrp6p central fragment, residues 129-536 / Mutation: Y361A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP6 / Plasmid: pET30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta
References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12-14% PEG 20000, 0.1M Mes or Hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.5 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2005 / Details: Si mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.25→36.22 Å / Num. all: 27056 / Num. obs: 27056 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 50.455 Å2 / Rmerge(I) obs: 0.04 / Χ2: 1.077 / Net I/σ(I): 19.7
Reflection shellResolution: 2.25→2.33 Å / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.9 / Num. unique all: 2637 / Num. unique obs: 2637 / Χ2: 1.31 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
MAR345data collection
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2HBJ

2hbj


Resolution: 2.25→36.22 Å / FOM work R set: 0.798 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2646 9.8 %RANDOM
Rwork0.222 ---
all0.228 26390 --
obs0.228 26390 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.103 Å2
Displacement parametersBiso mean: 57.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.328 Å2-0.329 Å20 Å2
2--3.328 Å20 Å2
3----6.656 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.25→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 2 252 3470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27073
X-RAY DIFFRACTIONc_bond_d0.00697
X-RAY DIFFRACTIONc_dihedral_angle_d22.06509
X-RAY DIFFRACTIONc_improper_angle_d0.85941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.25-2.270.374490.316435484
2.27-2.280.325360.268454490
2.28-2.30.349370.309432469
2.3-2.310.388580.307469527
2.31-2.330.413620.296408470
2.33-2.350.32390.274471510
2.35-2.370.295550.276442497
2.37-2.380.376540.287425479
2.38-2.40.374530.284472525
2.4-2.420.313510.27462513
2.42-2.440.352550.263439494
2.44-2.470.391380.273470508
2.47-2.490.331540.284469523
2.49-2.510.394470.269456503
2.51-2.530.385540.286465519
2.53-2.560.348480.266489537
2.56-2.580.324620.239456518
2.58-2.610.298490.236466515
2.61-2.640.282720.233448520
2.64-2.670.314520.25485537
2.67-2.70.384520.271472524
2.7-2.730.308520.234475527
2.73-2.760.35460.269496542
2.76-2.80.36400.248469509
2.8-2.830.289500.234516566
2.83-2.870.258580.243428486
2.87-2.910.35580.219477535
2.91-2.960.302600.234486546
2.96-30.282570.226475532
3-3.050.339450.252491536
3.05-3.110.288510.26492543
3.11-3.160.293610.259485546
3.16-3.220.297440.245483527
3.22-3.290.324680.257466534
3.29-3.360.354490.257493542
3.36-3.440.249500.232487537
3.44-3.530.269670.266477544
3.53-3.620.286670.244477544
3.62-3.730.318500.213479529
3.73-3.850.258640.228482546
3.85-3.980.241480.192508556
3.98-4.140.236580.179479537
4.14-4.330.244530.188490543
4.33-4.560.209490.17502551
4.56-4.850.169520.148507559
4.85-5.220.19580.156492550
5.22-5.750.254460.184504550
5.75-6.580.285570.233496553
6.58-8.290.308550.217517572
8.29-500.010.249560.196530586
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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