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- PDB-7q4l: The solution structure of hsDND1 RRM12 bound to CUUAUUUG RNA -

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Basic information

Entry
Database: PDB / ID: 7q4l
TitleThe solution structure of hsDND1 RRM12 bound to CUUAUUUG RNA
Components
  • Dead end protein homolog 1
  • RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')
KeywordsRNA BINDING PROTEIN / Protein-RNA complex / post-transcriptional gene regulation / PTGR / germ line differentiation / AU-rich RNA binding protein
Function / homology
Function and homology information


negative regulation of miRNA-mediated gene silencing / 3'-UTR-mediated mRNA destabilization / mRNA stabilization / germ cell development / mRNA 3'-UTR binding / mRNA binding / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Dead end protein 1, RNA recognition motif 1 / DND1, double-stranded RNA binding 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
Similarity search - Domain/homology
RNA / Dead end protein homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDuszczyk, M.M. / Allain, F.H.T.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_149921 Switzerland
Swiss National Science Foundation31003A_170130 Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: The solution structure of Dead End bound to AU-rich RNA reveals an unusual mode of tandem RRM-RNA recognition required for mRNA regulation.
Authors: Duszczyk, M.M. / Wischnewski, H. / Kazeeva, T. / Arora, R. / Loughlin, F.E. / von Schroetter, C. / Pradere, U. / Hall, J. / Ciaudo, C. / Allain, F.H.
History
DepositionOct 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: 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.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dead end protein homolog 1
B: RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)27,3932
Polymers27,3932
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations and lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Dead end protein homolog 1 / RNA-binding motif / single-stranded-interacting protein 4


Mass: 24927.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DND1, RBMS4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IYX4
#2: RNA chain RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')


Mass: 2465.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic32D 1H-15N HSQC
125isotropic32D 1H-13C HSQC
132isotropic33D 1H-15N NOESY
141isotropic23D HNCO TROSY
151isotropic23D HN(CA)CO TROSY
165isotropic33D 1H-15N NOESY
171isotropic23D HN(CO)CACB TROSY
181isotropic23D HN(CA)CB TROSY
191isotropic23D HN(CO)CA TROSY
1101isotropic23D HNCA TROSY
1112isotropic32D 1H-13C HSQC
1125isotropic32D F1 filtered, F2 filtered NOESY
1135isotropic32D F2 filtered NOESY
1143isotropic32D NOESY
1153isotropic12D TOCSY
1165isotropic13D (H)CCH-COSY
1175isotropic13D (H)CCH-TOCSY
1185isotropic13D (H)CCH-TOCSY
1195isotropic33D 1H-13C-HSQC-aromatic-NOESY
1205isotropic33D 1H-13C-HMQC-NOESY
1216isotropic32D 1H-13C HSQC
1224isotropic32D 1H-13C HSQC
1238isotropic32D F2 filtered NOESY
1247isotropic32D F2 filtered NOESY
1258isotropic32D F1 filtered, F2 filtered NOESY
1267isotropic32D F1 filtered, F2 filtered NOESY
1273isotropic32D 1H-1H TOCSY
1285isotropic33D F3 filtered, F2 edited 13C HMQC-NOESY
1295isotropic32D 13C F2 filtered 2D NOESY
1305isotropic32D 13C F1 filtered, F2 filtered NOESY
1319anisotropic22D 1H-15N TROSY
13211isotropic22D 1H-15N TROSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM fractionally deuterated, 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 95% H2O/5% D2O13C15NfracdeutRRM12-CUUAUUUG95% H2O/5% D2O
solution20.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 95% H2O/5% D2O13C15NRRM12-CUUAUUUG_H2O95% H2O/5% D2O
solution30.8 mM hsDnd1 RRM12, 0.8 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 100% D2ORRM12-CUUAUUUG100% D2O
solution40.8 mM hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled C*UU*AU*UU*G RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 100% D2ORRM12-C*UU*AU*UU*G100% D2O
solution50.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 100% D2O13C15NRRM12-CUUAUUUG_D2O100% D2O
solution60.8 mM hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled CU*UA*UU*UG* RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 100% D2ORRM12-CU*UA*UU*UG*100% D2O
solution70.8 mM 13C15N hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled C*UU*AU*UU*G RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 100% D2O13C15NRRM12-C*UU*AU*UU*G100% D2O
solution80.8 mM 13C15N hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled CU*UA*UU*UG* RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 100% D2O13C15NRRM12-CU*UA*UU*UG*100% D2O
solution90.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 4.2 % C12E5 polyethylene glycol / hexanol, 95% H2O/5% D2O15NRRM12-CUUAUUUG_H2O_aniso95% H2O/5% D2O
solution110.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 95% H2O/5% D2O15NRRM12-CUUAUUUG_H2O_iso95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMhsDnd1 RRM12fractionally deuterated, 13C,15N-labeled1
0.9 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')none1
100 mMKHPO4/ KH2PO4 pH 6.6none1
1 mMDTTnone1
0.8 mMhsDnd1 RRM1213C,15N-labeled2
0.9 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')none2
100 mMKHPO4/ KH2PO4 pH 6.6none2
1 mMDTTnone2
0.8 mMhsDnd1 RRM12none3
0.8 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')none3
100 mMKHPO4/ KH2PO4 pH 6.6none3
1 mMDTTnone3
0.8 mMhsDnd1 RRM12none4
0.8 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')selectively 13C ribose-labeled C*UU*AU*UU*G4
100 mMKHPO4/ KH2PO4 pH 6.6none4
1 mMDTTnone4
0.8 mMhsDnd1 RRM1213C,15N-labeled5
0.9 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')none5
100 mMKHPO4/ KH2PO4 pH 6.6none5
1 mMDTTnone5
0.8 mMhsDnd1 RRM12none6
0.8 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')selectively 13C ribose-labeled CU*UA*UU*UG*6
100 mMKHPO4/ KH2PO4 pH 6.6none6
1 mMDTTnone6
0.8 mMhsDnd1 RRM1213C15N7
0.8 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')selectively 13C ribose-labeled C*UU*AU*UU*G7
100 mMKHPO4/ KH2PO4 pH 6.6none7
1 mMDTTnone7
0.8 mMhsDnd1 RRM1213C15N8
0.8 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')selectively 13C ribose-labeled CU*UA*UU*UG*8
100 mMKHPO4/ KH2PO4 pH 6.6none8
1 mMDTTnone8
0.8 mMhsDnd1 RRM1213C,15N-labeled9
0.9 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')none9
100 mMKHPO4/ KH2PO4 pH 6.6none9
1 mMDTTnone9
4.2 %C12E5 polyethylene glycol / hexanolnone9
0.8 mMhsDnd1 RRM1213C,15N-labeled11
0.9 mMRNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')none11
100 mMKHPO4/ KH2PO4 pH 6.6none11
1 mMDTTnone11
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.6 / Pressure: AMBIENT atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKY1.1412Lee W, Tonelli M, Markley JLdata analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
ATNOS3.1ATNOS-CANDIDpeak picking
SparkyGoddardchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations and lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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