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- PDB-7qdd: NMR structure of Npl3 RRM1 bound to the AUCCAA RNA -

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Basic information

Entry
Database: PDB / ID: 7qdd
TitleNMR structure of Npl3 RRM1 bound to the AUCCAA RNA
Components
  • Nucleolar protein 3
  • RNA (5'-R(*AP*UP*CP*CP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / splicing / U2 snRNA / RRM / split-iCRAC / yeast / protein-RNA complex
Function / homology
Function and homology information


negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / eukaryotic initiation factor 4G binding / double-stranded telomeric DNA binding / telomeric repeat-containing RNA binding / poly(A) binding / RNA polymerase II complex binding / translational termination / positive regulation of transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / cytoplasmic stress granule ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / eukaryotic initiation factor 4G binding / double-stranded telomeric DNA binding / telomeric repeat-containing RNA binding / poly(A) binding / RNA polymerase II complex binding / translational termination / positive regulation of transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / cytoplasmic stress granule / ribosome biogenesis / negative regulation of translation / ribonucleoprotein complex / mRNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Npl3, RNA recognition motif 1 / : / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits ...Npl3, RNA recognition motif 1 / : / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Serine/arginine (SR)-type shuttling mRNA binding protein NPL3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsClery, A. / Allain, F.H.-T. / Moursy, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B-189379 Switzerland
Citation
Journal: Nat Commun / Year: 2023
Title: RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing.
Authors: Moursy, A. / Clery, A. / Gerhardy, S. / Betz, K.M. / Rao, S. / Mazur, J. / Campagne, S. / Beusch, I. / Duszczyk, M.M. / Robinson, M.D. / Panse, V.G. / Allain, F.H.
#1: Journal: Biorxiv / Year: 2022
Title: The structure of yeast Npl3 bound to RNA reveals a cooperative sequence-specific recognition and an RNA chaperone role in splicing
Authors: Moursy, A. / Clery, A. / Gerhardy, S. / Betz, K.M. / Rao, S. / Campagne, S. / Beusch, I. / Duszczyk, M.M. / Robinson, M.D. / Panse, V.G. / Allain, F.H.T.
History
DepositionNov 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*AP*UP*CP*CP*AP*A)-3')
B: Nucleolar protein 3


Theoretical massNumber of molelcules
Total (without water)11,9812
Polymers11,9812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1500 Å2
ΔGint-2 kcal/mol
Surface area6180 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*AP*UP*CP*CP*AP*A)-3')


Mass: 1859.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic RNA from horizon / Source: (synth.) synthetic construct (others)
#2: Protein Nucleolar protein 3 / Mitochondrial targeting suppressor 1 protein / Nuclear polyadenylated RNA-binding protein 1


Mass: 10121.476 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: recombinant protein
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NPL3, MTR13, MTS1, NAB1, NOP3, YDR432W, D9461.19 / Production host: unidentified plasmid (others) / References: UniProt: Q01560

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
122isotropic13D 1H-13C NOESY aliphatic
132isotropic13D 1H-13C NOESY aromatic
141isotropic22D NOESY
152isotropic32D NOESY F1fF2f
162isotropic32D NOESY F2f
172isotropic23D HN(CA)CB

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.9 mM [U-15N] Npl3 RRM1, 90% H2O/10% D2O15N Npl3 RRM190% H2O/10% D2O
solution20.9 mM [U-100% 13C; U-100% 15N] Npl3 RRM1, 90% H2O/10% D2O15N 13C Npl3 RRM190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMNpl3 RRM1[U-15N]1
0.9 mMNpl3 RRM1[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 50 mM / Label: standard / pH: 6.9 Not defined / Pressure: 0 Pa / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCE III HDBrukerAVANCE III HD7002
Bruker AVANCE III HDBrukerAVANCE III HD6003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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