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- PDB-5mpl: hnRNP A1 RRM2 in complex with 5'-UCAGUU-3' RNA -

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Basic information

Entry
Database: PDB / ID: 5mpl
TitlehnRNP A1 RRM2 in complex with 5'-UCAGUU-3' RNA
Components
  • Heterogeneous nuclear ribonucleoprotein A1
  • RNA UCAGUU
KeywordsSPLICING / RRM / RNA / hnRNP
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / pre-mRNA binding / G-rich strand telomeric DNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / pre-mRNA binding / G-rich strand telomeric DNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of telomere maintenance via telomerase / mRNA transport / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / 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 ...hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / 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
RNA / Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBarraud, P. / Allain, F.H.-T.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR structural biology Switzerland
Swiss National Science FoundationNCCR RNA and disease Switzerland
CitationJournal: Elife / Year: 2017
Title: Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7.
Authors: Beusch, I. / Barraud, P. / Moursy, A. / Clery, A. / Allain, F.H.
History
DepositionDec 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein A1
B: RNA UCAGUU


Theoretical massNumber of molelcules
Total (without water)13,4832
Polymers13,4832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1770 Å2
ΔGint-3 kcal/mol
Surface area6850 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #15medoid

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein A1 / hnRNP A1 / Helix-destabilizing protein / Single-strand RNA-binding protein / hnRNP core protein A1


Mass: 11630.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1, HNRPA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09651
#2: RNA chain RNA UCAGUU


Mass: 1853.133 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
111isotropic22D 1H-15N HSQC
124isotropic52D 1H-13C HSQC aliphatic
134isotropic32D 1H-13C HSQC aromatic
142isotropic13D HNCA
152isotropic13D HN(CA)CB
162isotropic13D CBCA(CO)NH
172isotropic13D HNCO
182isotropic43D HCc(CO)NH TOCSY
192isotropic43D hCC(CO)NH TOCSY
1101isotropic53D 1H-15N NOESY
1112isotropic53D 1H-13C NOESY aliphatic
1122isotropic53D 1H-13C NOESY aromatic
1173isotropic52D 1H-1H NOESY
1163isotropic22D 1H-1H TOCSY
1154isotropic42D F1fF2f 13C-filtered NOESY
1144isotropic23D F1eF3f 13C-filtered/edited NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 15N] hnRNP A1 RRM2, 1.0 g/L RNA UCAGUU, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21.0 mM [U-99% 13C; U-99% 15N] hnRNP A1 RRM2, 1.0 mM RNA UCAGUU, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution31.0 mM [U-99% 15N] hnRNP A1 RRM2, 1.0 mM RNA UCAGUU, 100% D2O15N_sample_D2O100% D2O
solution41.0 mM [U-99% 13C; U-99% 15N] hnRNP A1 RRM2, 1.0 mM RNA UCAGUU, 100% D2O13C15N_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMhnRNP A1 RRM2[U-99% 15N]1
1.0 g/LRNA UCAGUUnatural abundance1
1.0 mMhnRNP A1 RRM2[U-99% 13C; U-99% 15N]2
1.0 mMRNA UCAGUUnatural abundance2
1.0 mMhnRNP A1 RRM2[U-99% 15N]3
1.0 mMRNA UCAGUUnatural abundance3
1.0 mMhnRNP A1 RRM2[U-99% 13C; U-99% 15N]4
1.0 mMRNA UCAGUUnatural abundance4
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III7004
Bruker AVANCE IIIBrukerAVANCE III7503
Bruker AVANCEBrukerAVANCE9005

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
PROCHECK / PROCHECK-NMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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