+Open data
-Basic information
Entry | Database: PDB / ID: 7qdd | ||||||
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Title | NMR structure of Npl3 RRM1 bound to the AUCCAA RNA | ||||||
Components |
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Keywords | RNA 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 / 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 ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / eukaryotic initiation factor 4G 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 | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Clery, A. / Allain, F.H.-T. / Moursy, A. | ||||||
Funding support | Switzerland, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qdd.cif.gz | 322.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qdd.ent.gz | 267.7 KB | Display | PDB format |
PDBx/mmJSON format | 7qdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qdd_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 7qdd_full_validation.pdf.gz | 507 KB | Display | |
Data in XML | 7qdd_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 7qdd_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/7qdd ftp://data.pdbj.org/pub/pdb/validation_reports/qd/7qdd | HTTPS FTP |
-Related structure data
Related structure data | 7qdeC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 1859.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic RNA from horizon / Source: (synth.) synthetic construct (others) |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50 mM / Label: standard / pH: 6.9 Not defined / Pressure: 0 Pa / Temperature: 313 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 |