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- PDB-5szw: NMR solution structure of the RRM1 domain of the post-transcripti... -

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Basic information

Entry
Database: PDB / ID: 5szw
TitleNMR solution structure of the RRM1 domain of the post-transcriptional regulator HuR
ComponentsELAV-like protein 1
KeywordsRNA BINDING PROTEIN / RNA-binding protein Post-trasncriptional regulation RNA recognition motif
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / lncRNA binding / miRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization ...HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / lncRNA binding / miRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization / sarcoplasm / positive regulation of superoxide anion generation / mRNA 3'-UTR binding / positive regulation of translation / P-body / protein homooligomerization / cytoplasmic stress granule / protein import into nucleus / double-stranded RNA binding / cytoplasmic vesicle / postsynapse / ribonucleoprotein complex / mRNA binding / glutamatergic synapse / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / 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 ...HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLixa, C. / Mujo, A. / Jendiroba, K.A. / Almeida, F.C.L. / Lima, L.M.T.R. / Pinheiro, A.S.
Funding support Brazil, United States, 3items
OrganizationGrant numberCountry
FAPERJ Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Brown University Brazil Initiative Colaboration Grant United States
Citation
Journal: J. Biomol. NMR / Year: 2018
Title: Oligomeric transition and dynamics of RNA binding by the HuR RRM1 domain in solution.
Authors: Lixa, C. / Mujo, A. / de Magalhaes, M.T.Q. / Almeida, F.C.L. / Lima, L.M.T.R. / Pinheiro, A.S.
#1: Journal: Biomol NMR Assign / Year: 2015
Title: (1)H, (15)N and (13)C resonance assignments of the RRM1 domain of the key post-transcriptional regulator HuR.
Authors: Mujo, A. / Lixa, C. / Carneiro, L.A. / Anobom, C.D. / Almeida, F.C. / Pinheiro, A.S.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_ensemble / pdbx_nmr_representative
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)11,2211
Polymers11,2211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ELAV-like protein 1 / Hu-antigen R / HuR


Mass: 11220.585 Da / Num. of mol.: 1 / Fragment: UNP residues 28-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELAVL1, HUR / Plasmid: RP1B
Details (production host): Recombinant protein expressed in fusion with a Thio6His6 expression/purification tag, followed by a TEV protease cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15717

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
122isotropic12D 1H-13C HSQC aliphatic
132isotropic12D 1H-13C HSQC aromatic
142isotropic13D HN(CA)CB
152isotropic13D CBCA(CO)NH
192isotropic13D HNCO
182isotropic13D HN(CA)CO
172isotropic13D HBHA(CO)NH
162isotropic23D (H)CC(CO)NH
1102isotropic13D (H)CCH-TOCSY
1112isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.5 mM [U-15N] HuR_RRM1, 30 mM sodium phosphate, 100 mM sodium chloride, 10 mM DTT, 90% H2O/10% D2OU-100% 15N; 1.5mMRRM1_N1590% H2O/10% D2O
solution21.5 mM [U-100% 13C; U-100% 15N] HuR_RRM1, 30 mM sodium phosphate, 100 mM sodium chloride, 10 mM DTT, 90% H2O/10% D2OU-100% 13C; U-100% 15N; 1.5mMRRM1_N15_C1390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMHuR_RRM1[U-15N]1
30 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
10 mMDTTnatural abundance1
1.5 mMHuR_RRM1[U-100% 13C; U-100% 15N]2
30 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
10 mMDTTnatural abundance2
Sample conditionsIonic strength: 100 mM / Label: Conditions_RRM1 / pH: 6.0 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CcpNMRCCPNdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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