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

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Basic information

Entry
Database: PDB / ID: 2hbl
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 AMP
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
ADENOSINE MONOPHOSPHATE / : / Exosome complex exonuclease RRP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _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.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

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Assembly

Deposited unit
A: Exosome complex exonuclease RRP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1434
Polymers47,6751
Non-polymers4683
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.846, 110.846, 79.873
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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.97 Å3/Da / Density % sol: 58.58 %
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: MAX II / Beamline: I911-5 / Wavelength: 1.043 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2005 / Details: Si mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 2.3→36.87 Å / Num. all: 25647 / Num. obs: 25647 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 53.697 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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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: 2.3→36.87 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2459 9.6 %RANDOM
Rwork0.239 ---
all0.243 24433 --
obs0.243 24433 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.6 Å2
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.211 Å2-1.332 Å20 Å2
2--3.211 Å20 Å2
3----6.423 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 25 127 3368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006643
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.23772
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.93637
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used
2.3-2.320.354570.323442X-RAY DIFFRACTION49
2.32-2.330.377600.33373X-RAY DIFFRACTION49
2.33-2.350.356350.318427X-RAY DIFFRACTION49
2.35-2.370.356520.321404X-RAY DIFFRACTION49
2.37-2.380.299430.315402X-RAY DIFFRACTION49
2.38-2.40.355580.338407X-RAY DIFFRACTION49
2.4-2.420.429340.34404X-RAY DIFFRACTION49
2.42-2.440.289460.305419X-RAY DIFFRACTION49
2.44-2.460.323430.295416X-RAY DIFFRACTION49
2.46-2.480.349390.287417X-RAY DIFFRACTION49
2.48-2.50.354430.29431X-RAY DIFFRACTION49
2.5-2.530.344440.277431X-RAY DIFFRACTION49
2.53-2.550.372440.3427X-RAY DIFFRACTION49
2.55-2.570.318550.287445X-RAY DIFFRACTION49
2.57-2.60.35540.259429X-RAY DIFFRACTION49
2.6-2.620.359520.283442X-RAY DIFFRACTION49
2.62-2.650.378580.301418X-RAY DIFFRACTION49
2.65-2.680.32450.29453X-RAY DIFFRACTION49
2.68-2.710.36500.261428X-RAY DIFFRACTION49
2.71-2.740.309490.267473X-RAY DIFFRACTION49
2.74-2.770.334440.289444X-RAY DIFFRACTION49
2.77-2.810.391360.277440X-RAY DIFFRACTION49
2.81-2.840.261490.25478X-RAY DIFFRACTION49
2.84-2.880.314530.273398X-RAY DIFFRACTION49
2.88-2.920.282530.251463X-RAY DIFFRACTION49
2.92-2.960.338550.251450X-RAY DIFFRACTION49
2.96-30.239550.243453X-RAY DIFFRACTION49
3-3.050.308400.253458X-RAY DIFFRACTION49
3.05-3.10.319530.274480X-RAY DIFFRACTION49
3.1-3.150.284540.272432X-RAY DIFFRACTION49
3.15-3.210.329420.268482X-RAY DIFFRACTION49
3.21-3.270.377600.274440X-RAY DIFFRACTION49
3.27-3.340.33570.275473X-RAY DIFFRACTION49
3.34-3.410.307490.262475X-RAY DIFFRACTION49
3.41-3.490.308510.281455X-RAY DIFFRACTION49
3.49-3.580.301660.272461X-RAY DIFFRACTION49
3.58-3.680.292620.257456X-RAY DIFFRACTION49
3.68-3.780.301510.243463X-RAY DIFFRACTION49
3.78-3.910.298530.236472X-RAY DIFFRACTION49
3.91-4.050.258530.217461X-RAY DIFFRACTION49
4.05-4.210.259540.197468X-RAY DIFFRACTION49
4.21-4.40.267480.207483X-RAY DIFFRACTION49
4.4-4.630.24490.174479X-RAY DIFFRACTION49
4.63-4.920.16510.177465X-RAY DIFFRACTION49
4.92-5.30.238520.174486X-RAY DIFFRACTION49
5.3-5.840.265480.213482X-RAY DIFFRACTION49
5.84-6.680.299580.248479X-RAY DIFFRACTION49
6.68-8.420.261480.21493X-RAY DIFFRACTION49
8.42-500.010.262540.177517X-RAY DIFFRACTION49
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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