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- PDB-7pvm: NMR structure of the C. thermophilum Xrn2 zinc finger -

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Basic information

Entry
Database: PDB / ID: 7pvm
TitleNMR structure of the C. thermophilum Xrn2 zinc finger
Components5'-3' exoribonuclease
KeywordsRNA BINDING PROTEIN / Zinc finger
Function / homology
Function and homology information


negative regulation of phosphorylation of RNA polymerase II C-terminal domain / RNA polymerase II termination complex / tRNA surveillance / Las1 complex / positive regulation of termination of RNA polymerase II transcription / nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' / positive regulation of chromosome segregation / termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent / nuclear polyadenylation-dependent rRNA catabolic process ...negative regulation of phosphorylation of RNA polymerase II C-terminal domain / RNA polymerase II termination complex / tRNA surveillance / Las1 complex / positive regulation of termination of RNA polymerase II transcription / nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' / positive regulation of chromosome segregation / termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent / nuclear polyadenylation-dependent rRNA catabolic process / sno(s)RNA processing / 5'-3' exoribonuclease activity / nuclear mRNA surveillance / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of transcription elongation by RNA polymerase II / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / rRNA binding
Similarity search - Function
5'-3' exoribonuclease type 2 / Xrn1, helical domain / 5'-3' exoribonuclease / Xrn1 helical domain / Xrn1, N-terminal / XRN 5'-3' exonuclease N-terminus
Similarity search - Domain/homology
5'-3' exoribonuclease
Similarity search - Component
Biological speciesChaetomium thermophilum (unknown)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsOverbeck, J.H. / Sprangers, R. / Wurm, J.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Observation of conformational changes that underlie the catalytic cycle of Xrn2.
Authors: Overbeck, J.H. / Stelzig, D. / Fuchs, A.L. / Wurm, J.P. / Sprangers, R.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-3' exoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3762
Polymers3,3111
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3620 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein/peptide 5'-3' exoribonuclease


Mass: 3310.810 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (unknown)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0008830 / Production host: Escherichia coli (E. coli)
References: UniProt: G0S058, 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
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D HN(CA)CO
151isotropic13D H(CCO)NH
161isotropic13D C(CO)NH
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY
191isotropic22D 1H-13C HSQC
1101isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 25 mM HEPES, 125 mM NaCl, 0.03 % NaN3, 95% H2O/5% D2O
Label: sample1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMHEPESnatural abundance1
125 mMNaClnatural abundance1
0.03 %NaN3natural abundance1
Sample conditionsIonic strength: 125 mM / Label: conditions1 / pH: 7.3 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO5001
Bruker AVANCE NEOBrukerAVANCE NEO6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
NMRFAM-SPARKY1.414W. Leepeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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