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- PDB-2my8: NMR Structure of RRM-3 domain of ETR-3 -

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Basic information

Entry
Database: PDB / ID: 2my8
TitleNMR Structure of RRM-3 domain of ETR-3
ComponentsCUGBP Elav-like family member 2
KeywordsRNA BINDING PROTEIN / ETR3 RRM-3
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 / 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 ...CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / Paraneoplastic encephalomyelitis antigen / 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
CUGBP Elav-like family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
AuthorsKashyap, M. / Bhatt, H.P. / Ganguly, A.K. / Bhavesh, N.S.
CitationJournal: Biophys.J. / Year: 2020
Title: Structure of an Unfolding Intermediate of an RRM Domain of ETR-3 Reveals Its Native-like Fold.
Authors: Bhatt, H. / Ganguly, A.K. / Sharma, S. / Kushwaha, G.S. / Firoz Khan, M. / Sen, S. / Bhavesh, N.S.
History
DepositionJan 21, 2015Deposition site: BMRB / Processing site: RCSB
SupersessionFeb 4, 2015ID: 2MIL
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 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: CUGBP Elav-like family member 2


Theoretical massNumber of molelcules
Total (without water)10,9311
Polymers10,9311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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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: 10930.555 Da / Num. of mol.: 1 / Fragment: UNP residues 416-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CELF2, BRUNOL3, CUGBP2, ETR3, NAPOR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95319

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D H(CCO)NH
1813D C(CO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D HNN
11313D HN(C)N

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Sample preparation

DetailsContents: 1-1.2 mM [U-13C; U-15N] RRM3, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRRM3-1[U-13C; U-15N]1-1.21
20 mMsodium phosphate-21
50 mMsodium chloride-31
0.1 %sodium azide-41
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1 / Details: WATER REFINEMENT
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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