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- PDB-6y96: solution structure of cold-shock domain 9 of drosophila Upstream ... -

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Basic information

Entry
Database: PDB / ID: 6y96
Titlesolution structure of cold-shock domain 9 of drosophila Upstream of N-Ras (Unr)
ComponentsUpstream of N-ras, isoform A
KeywordsRNA BINDING PROTEIN / CSD / RBP
Function / homology
Function and homology information


dosage compensation complex assembly / protein-RNA adaptor activity / RISC complex binding / sex differentiation / lncRNA binding / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cell differentiation / RNA binding / cytosol
Similarity search - Function
: / Cold shock domain-containing protein E1 CSD domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins ...: / Cold shock domain-containing protein E1 CSD domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA-binding protein Unr
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsSweetapple, L.J. / Hollmann, N.M. / Simon, B. / Hennig, J.
CitationJournal: Cell Rep / Year: 2020
Title: Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras.
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Masiewicz, P. / Guitart, T. / Simon, B. / Provaznik, J. / Stein, F. / Haberkant, P. / Sweetapple, L.J. / Villacorta, L. / Mooijman, D. / Benes, V. / ...Authors: Hollmann, N.M. / Jagtap, P.K.A. / Masiewicz, P. / Guitart, T. / Simon, B. / Provaznik, J. / Stein, F. / Haberkant, P. / Sweetapple, L.J. / Villacorta, L. / Mooijman, D. / Benes, V. / Savitski, M.M. / Gebauer, F. / Hennig, J.
History
DepositionMar 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 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

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Assembly

Deposited unit
A: Upstream of N-ras, isoform A


Theoretical massNumber of molelcules
Total (without water)10,2471
Polymers10,2471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6470 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Upstream of N-ras, isoform A


Mass: 10246.532 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the first two residues (GA) are leftovers from the cleavage/cloning sequence
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Unr, BcDNA:LD13080, CR32028, Dmel\CG7015, dUNR, MRE30, UNR, unr, CG7015, Dmel_CG7015
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VSK3

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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
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
182isotropic22D 1H-13C HSQC aliphatic
171isotropic13D HBHA(CO)NH
162isotropic23D (H)CCH-TOCSY
192isotropic22D 1H-1H NOESY
1112isotropic23D 1H-13C NOESY
1101isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.24 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2OdCSD9_H2O95% H2O/5% D2O
solution20.24 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 100% D2OdCSD9_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.24 mMprotein[U-99% 13C; U-99% 15N]1
50 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
0.24 mMprotein[U-99% 13C; U-99% 15N]2
50 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
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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