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- PDB-7prd: Solution structure of the chimeric Nrd1-Nab3 heterodimerization d... -

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Basic information

Entry
Database: PDB / ID: 7prd
TitleSolution structure of the chimeric Nrd1-Nab3 heterodimerization domains
ComponentsProtein NRD1,HLJ1_G0022400.mRNA.1.CDS.1
KeywordsTRANSCRIPTION / Transcription termination / NNS pathway / Nab3 / Nrd1 / heterodimerization / chimera / yeast
Function / homology
Function and homology information


Nab3, RNA recognition motif / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / Anticodon-binding domain superfamily / RNA recognition motif / RNA recognition motif ...Nab3, RNA recognition motif / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / Anticodon-binding domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
HLJ1_G0022400.mRNA.1.CDS.1 / Protein NRD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsChaves-Arquero, B. / Martinez-Lumbreras, S. / Perez-Canadillas, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Autonomous Community of MadridBMD-3770 Spain
CitationJournal: Life Sci Alliance / Year: 2022
Title: Structural basis of Nrd1-Nab3 heterodimerization.
Authors: Chaves-Arquero, B. / Martinez-Lumbreras, S. / Camero, S. / Santiveri, C.M. / Mirassou, Y. / Campos-Olivas, R. / Jimenez, M.A. / Calvo, O. / Perez-Canadillas, J.M.
History
DepositionSep 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein NRD1,HLJ1_G0022400.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)13,9441
Polymers13,9441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1medoid

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Components

#1: Protein Protein NRD1,HLJ1_G0022400.mRNA.1.CDS.1


Mass: 13943.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCNYR20_0008007600, SCP684_0008007200, PACBIOSEQ_LOCUS5883
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6V8SAW3, UniProt: A0A6L0ZXA8

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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
122isotropic12D 1H-13C HSQC
131isotropic13D HNCA
141isotropic13D HNCO
151isotropic13D CBCA(CO)NH
161isotropic13D HN(CA)CB
172isotropic13D (H)CCH-TOCSY
184isotropic12D 1H-1H NOESY
195isotropic12D 1H-1H NOESY
1101isotropic13D 1H-15N NOESY
1113isotropic13D 1H-13C NOESY
1123isotropic13D 1H-13C HSQC NOESY 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDLabelSolvent system
solution1CN_H2O90% H2O/10% D2O
solution2CN_D2O100% D2O
solution3methyl-lab100% D2O
solution4na_H2O90% H2O/10% D2O
solution5na_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium acetatenatural abundance1
25 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
1000 uMNrd1-Nab3 chimera[U-100% 13C; U-100% 15N]1
10 mMsodium acetatenatural abundance2
25 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
1000 uMNrd1-Nab3 chimera[U-100% 13C; U-100% 15N]2
10 mMsodium acetatenatural abundance3
25 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
1000 uMNrd1-Nab3 chimera13C - methyl (IVL)3
10 mMsodium acetatenatural abundance4
25 mMsodium chloridenatural abundance4
1 mMDTTnatural abundance4
1000 uMNrd1-Nab3 chimeranatural abundance4
10 mMsodium acetatenatural abundance5
25 mMsodium chloridenatural abundance5
1 mMDTTnatural abundance5
1000 uMNrd1-Nab3 chimeranatural abundance5
Sample conditionsIonic strength: 35 mM / Label: Conditions_1 / pH: 5.1 / Pressure: 1 atm / 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
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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