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- PDB-7quu: Red1-Iss10 complex -

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Basic information

Entry
Database: PDB / ID: 7quu
TitleRed1-Iss10 complex
Components
  • NURS complex subunit red1
  • Uncharacterized protein C7D4.14c
KeywordsRNA / MTREC complex / RNA degradation / meiosis
Function / homology
Function and homology information


MTREC complex / nucleolar peripheral inclusion body / cleavage body / sno(s)RNA processing / regulation of siRNA-mediated facultative heterochromatin formation / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex ...MTREC complex / nucleolar peripheral inclusion body / cleavage body / sno(s)RNA processing / regulation of siRNA-mediated facultative heterochromatin formation / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / heterochromatin island / exosome (RNase complex) / protein-macromolecule adaptor activity / nuclear body / chromatin / nucleus / metal ion binding
Similarity search - Function
Putative zinc-finger domain / NURS complex subunit red1 / Putative zinc-finger domain
Similarity search - Domain/homology
Uncharacterized protein C7D4.14c / NURS complex subunit red1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsMackereth, C.D. / Kadlec, J. / Laroussi, H.
Funding support France, 3items
OrganizationGrant numberCountry
ATIP-Avenir France
Agence Nationale de la Recherche (ANR) France
Centre National de la Recherche Scientifique (CNRS)IR-RMN-THC Fr3050 France
CitationJournal: Nat Commun / Year: 2022
Title: Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex.
Authors: Foucher, A.E. / Touat-Todeschini, L. / Juarez-Martinez, A.B. / Rakitch, A. / Laroussi, H. / Karczewski, C. / Acajjaoui, S. / Soler-Lopez, M. / Cusack, S. / Mackereth, C.D. / Verdel, A. / Kadlec, J.
History
DepositionJan 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein C7D4.14c
B: NURS complex subunit red1


Theoretical massNumber of molelcules
Total (without water)11,8922
Polymers11,8922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein C7D4.14c


Mass: 6592.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC7D4.14c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14269
#2: Protein/peptide NURS complex subunit red1


Mass: 5299.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: red1, iss3, SPAC1006.03c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UTR8

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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
123isotropic22D 1H-13C HSQC
132isotropic13D HNCO
142isotropic13D HN(CA)CO
152isotropic13D HNCA
162isotropic13D HN(CA)CB
172isotropic13D CBCA(CO)NH
181isotropic13D HNHA
192isotropic13D HA(CACO)NH
1102isotropic13D H(CCO)NH
1112isotropic13D H(CCO)NH
1123isotropic23D (H)CCH-TOCSY
1133isotropic23D (H)CCH-TOCSY
1142isotropic13D 1H-15N NOESY
1152isotropic23D 1H-13C NOESY
1164isotropic12D 1H-1H TOCSY
1174isotropic12D DQF-COSY
1184isotropic12D 1H-1H NOESY
1191isotropic12D TROSY-RDC isotropic
1201anisotropic12D TROSY-RDC phage

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1150 uM [U-99% 15N] Red1, 150 uM [U-99% 15N] Iss10, 20 mM TRIS, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O15N_H2O90% H2O/10% D2O
solution2500 uM [U-99% 13C; U-99% 15N] Red1, 500 uM [U-99% 13C; U-99% 15N] Iss10, 20 mM TRIS, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O13C15N_H2O90% H2O/10% D2O
solution3500 uM [U-99% 13C; U-99% 15N] Red1, 500 uM [U-99% 13C; U-99% 15N] Iss10, 20 mM TRIS, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 100% D2O13C15N_D2O100% D2O
solution4150 uM [U-99% 13C; U-99% 15N] Red1, 150 uM [U-99% 13C; U-99% 15N] Iss10, 20 mM TRIS, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 100% D2O10c_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 uMRed1[U-99% 15N]1
150 uMIss10[U-99% 15N]1
20 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
5 mMbeta-mercaptoethanolnatural abundance1
500 uMRed1[U-99% 13C; U-99% 15N]2
500 uMIss10[U-99% 13C; U-99% 15N]2
20 mMTRISnatural abundance2
150 mMsodium chloridenatural abundance2
5 mMbeta-mercaptoethanolnatural abundance2
500 uMRed1[U-99% 13C; U-99% 15N]3
500 uMIss10[U-99% 13C; U-99% 15N]3
20 mMTRISnatural abundance3
150 mMsodium chloridenatural abundance3
5 mMbeta-mercaptoethanolnatural abundance3
150 uMRed1[U-99% 13C; U-99% 15N]4
150 uMIss10[U-99% 13C; U-99% 15N]4
20 mMTRISnatural abundance4
150 mMsodium chloridenatural abundance4
5 mMbeta-mercaptoethanolnatural abundance4
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE NEOBrukerAVANCE NEO7001PA TXI 700S4 H-C/N-D-05 Z BTO
Bruker AVANCE NEOBrukerAVANCE NEO8002TCI 800S6 H-C/N-D-05 Z P

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.0.6Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyNMRFAMGoddardchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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