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

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Basic information

Entry
Database: PDB / ID: 2hbm
TitleStructure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn, Zn, and UMP
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 / nuclear polyadenylation-dependent tRNA catabolic process / 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 / nuclear polyadenylation-dependent tRNA catabolic process / 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 / 3'-5' exonuclease ...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
: / URIDINE-5'-MONOPHOSPHATE / Exosome complex exonuclease RRP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 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.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.value / _struct_conn.pdbx_dist_value / _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_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)48,1204
Polymers47,6751
Non-polymers4453
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.577, 110.577, 79.330
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.93 Å3/Da / Density % sol: 58.09 %
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: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 9, 2006 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.7→29.61 Å / Num. all: 15522 / Num. obs: 15522 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 71.43 Å2 / Rmerge(I) obs: 0.061 / Χ2: 0.952 / Net I/σ(I): 14.9
Reflection shellResolution: 2.7→2.8 Å / % possible obs: 92.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1416 / Num. unique obs: 1416 / Χ2: 0.944 / % possible all: 92.9

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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
Resolution: 2.7→29.61 Å / FOM work R set: 0.796 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1465 9.3 %RANDOM
Rwork0.22 ---
all0.226 14609 --
obs0.226 14609 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.9 Å2
Displacement parametersBiso mean: 59.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.834 Å2-3.25 Å20 Å2
2--3.834 Å20 Å2
3----7.667 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 23 135 3374
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_bond_d0.007089
X-RAY DIFFRACTIONc_dihedral_angle_d22.56
X-RAY DIFFRACTIONc_improper_angle_d0.9053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.730.374390.332369408
2.73-2.770.392360.333363399
2.77-2.80.396280.334395423
2.8-2.840.307470.318382429
2.84-2.880.349490.312362411
2.88-2.920.471450.306425470
2.92-2.960.363490.283405454
2.96-3.010.325510.269427478
3.01-3.060.336450.262446491
3.06-3.110.299490.267450499
3.11-3.170.34580.296448506
3.17-3.230.361520.267439491
3.23-3.290.357610.264450511
3.29-3.360.305440.268463507
3.36-3.440.341510.251478529
3.44-3.530.289590.267451510
3.53-3.620.276680.245473541
3.62-3.730.346450.222483528
3.73-3.850.324670.233475542
3.85-3.990.255480.2491539
3.99-4.150.252550.185485540
4.15-4.340.307510.198476527
4.34-4.570.216460.164491537
4.57-4.850.188530.151495548
4.85-5.230.223590.163495554
5.23-5.750.264420.191496538
5.75-6.580.263610.222491552
6.58-8.30.269520.194513565
8.3-500.010.265550.167527582
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4dna-rna_rep.param

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