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- PDB-5m8i: Solution structure of CUG-BP2 RRM3 in complex with 5'-UUUAA-3' RNA -

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Basic information

Entry
Database: PDB / ID: 5m8i
TitleSolution structure of CUG-BP2 RRM3 in complex with 5'-UUUAA-3' RNA
Components
  • CUGBP Elav-like family member 2
  • RNA (5'-R(*UP*UP*UP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / RNA / RNA recognition motif
Function / homology
Function and homology information


mRNA splice site recognition / pre-mRNA binding / Flemming body / regulation of heart contraction / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / intracellular membrane-bounded organelle / RNA binding ...mRNA splice site recognition / pre-mRNA binding / Flemming body / regulation of heart contraction / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / intracellular membrane-bounded organelle / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / Paraneoplastic encephalomyelitis antigen / 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 / CUGBP Elav-like family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDiarra dit Konte, N. / Damberger, F.F. / Allain, F.H.T.
CitationJournal: Nat Commun / Year: 2017
Title: Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination.
Authors: Diarra Dit Konte, N. / Krepl, M. / Damberger, F.F. / Ripin, N. / Duss, O. / Sponer, J. / Allain, F.H.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CUGBP Elav-like family member 2
B: RNA (5'-R(*UP*UP*UP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,3752
Polymers14,3752
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1270 Å2
ΔGint-4 kcal/mol
Surface area8530 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy and least restraints violation
RepresentativeModel #1lowest energy

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Components

#1: Protein CUGBP Elav-like family member 2 / CELF-2 / Bruno-like protein 3 / CUG triplet repeat RNA-binding protein 2 / CUG-BP2 / CUG-BP- and ...CELF-2 / Bruno-like protein 3 / CUG triplet repeat RNA-binding protein 2 / CUG-BP2 / CUG-BP- and ETR-3-like factor 2 / ELAV-type RNA-binding protein 3 / ETR-3 / Neuroblastoma apoptosis-related RNA-binding protein / hNAPOR / RNA-binding protein BRUNOL-3


Mass: 12842.679 Da / Num. of mol.: 1 / Mutation: Y114W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CELF2, BRUNOL3, CUGBP2, ETR3, NAPOR / Production host: Escherichia coli (E. coli) / References: UniProt: O95319
#2: RNA chain RNA (5'-R(*UP*UP*UP*AP*A)-3')


Mass: 1531.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic52D 1H-15N HSQC
121isotropic52D 1H-13C HSQC aliphatic
131isotropic52D 1H-13C HSQC aromatic
141isotropic53D 1H-15N NOESY
151isotropic53D 1H-13C NOESY aliphatic
1142isotropic43D F1 13C-filtered 1H-1H NOESY 13C-1H HSQC aromatic
1132isotropic53D F1 13C-filtered 1H-1H NOESY 13C-1H HSQC aliphatic
1123isotropic5natural abundance 2D 13C-1H HSQC
1112isotropic52D F2 13C-filtered 1H-1H NOESY
1102isotropic52D 1H-1H NOESY
192isotropic52D 1H-1H TOCSY
181isotropic53D HNHA
171isotropic12D 1H-15N HSQC long range
161isotropic53D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.6 mM [U-99% 13C; U-99% 15N] CUG-BP2 third RNA Recognition Motif, 1.8 mM unlabeled 5'-UUUAA-3' RNA, 95% H2O/5% D2OCUG-BP2 RRM3 in complex with 5'-UUUAA-3' RNA; 1:3 protein:RNA ratio13C sample 1:395% H2O/5% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] CUG-BP2 third RNA Recognition Motif, 0.8 mM non-labeled 5'-UUUAA-3' RNA, 95% H2O/5% D2OCUG-BP2 RRM3 in complex with 5'-UUUAA-3' RNA; 1:1 protein:RNA ratio13C sample 1:195% H2O/5% D2O
solution30.8 mM [U-99% 15N] CUG-BP2 third RNA Recognition Motif, 0.8 mM non-labeled 5'-UUUAA-3' RNA, 95% H2O/5% D2OCUG-BP2 RRM3 in complex with 5'-UUUAA-3' RNA; 1:1 protein:RNA ratio15N sample 1:195% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMCUG-BP2 third RNA Recognition Motif[U-99% 13C; U-99% 15N]1
1.8 mM5'-UUUAA-3' RNAunlabeled1
0.8 mMCUG-BP2 third RNA Recognition Motif[U-99% 13C; U-99% 15N]2
0.8 mM5'-UUUAA-3' RNAnon-labeled2
0.8 mMCUG-BP2 third RNA Recognition Motif[U-99% 15N]3
0.8 mM5'-UUUAA-3' RNAnon-labeled3
Sample conditionsDetails: 10 mM NaCl, 20 mM K2HPO4/KH2PO4, beta-mercaptoethanol 0.1%, DEPC treated
Ionic strength: 130 mM / Label: condition / pH: 5.8 Not defined / Pressure: ambient Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7005
Bruker AVANCE IIIBrukerAVANCE III7504
Bruker AVANCE IIIBrukerAVANCE III9003
Bruker AVANCE III HDBrukerAVANCE III HD6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CANDIDHerrmann, Guntert and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and least restraints violation
Conformers calculated total number: 50 / Conformers submitted total number: 20

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