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- PDB-2cpr: Solution structure of the HRDC domain of human Exosome component 10 -

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Entry
Database: PDB / ID: 2cpr
TitleSolution structure of the HRDC domain of human Exosome component 10
ComponentsExosome component 10
KeywordsGENE REGULATION / HRDC / helix-bundle / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nucleolar exosome (RNase complex) / positive regulation of mRNA cis splicing, via spliceosome / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / RNA exonuclease activity / regulation of telomerase RNA localization to Cajal body / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process ...nucleolar exosome (RNase complex) / positive regulation of mRNA cis splicing, via spliceosome / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / RNA exonuclease activity / regulation of telomerase RNA localization to Cajal body / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / exosome (RNase complex) / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / 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) / histone mRNA catabolic process / nuclear mRNA surveillance / telomerase RNA binding / RNA catabolic process / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / maturation of 5.8S rRNA / negative regulation of telomere maintenance via telomerase / nuclear-transcribed mRNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / small-subunit processome / euchromatin / rRNA processing / ribosomal small subunit biogenesis / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / single-stranded RNA binding / DNA repair / nucleotide binding / nucleolus / RNA binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
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 / DNA polymerase; domain 1 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Exosome complex component 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dyanamics, simulated annealing
AuthorsNagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the HRDC domain of human Exosome component 10
Authors: Nagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exosome component 10


Theoretical massNumber of molelcules
Total (without water)13,9451
Polymers13,9451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Exosome component 10 / Polymyositis/scleroderma autoantigen 2 / Autoantigen PM/Scl 2 / Polymyositis/scleroderma ...Polymyositis/scleroderma autoantigen 2 / Autoantigen PM/Scl 2 / Polymyositis/scleroderma autoantigen 100 kDa / PM/Scl-100 / P100 polymyositis-scleroderma overlap syndrome associated autoantigen


Mass: 13945.032 Da / Num. of mol.: 1 / Fragment: HRDC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: EXOSC10 / Plasmid: P040906-09 / References: UniProt: Q01780

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.45mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801/20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.925Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dyanamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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