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- PDB-5mpg: Solution NMR structure of hnRNP A1 RRM1 in complex with 5'-UUAGGU... -

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Basic information

Entry
Database: PDB / ID: 5mpg
TitleSolution NMR structure of hnRNP A1 RRM1 in complex with 5'-UUAGGUC-3' RNA
Components
  • Heterogeneous nuclear ribonucleoprotein A1
  • RNA UUAGGUC
KeywordsSPLICING / RRM / RNA
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA 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 / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / localization / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / amyloid fibril formation / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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, France, 6items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR structural biology Switzerland
Swiss National Science FoundationNCCR RNA and disease Switzerland
CNRS France
ETHPostdoctoral ETH Fellowship Program Switzerland
Novartis Foundation Switzerland
SMA Europe 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 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3May 15, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,2022
Polymers13,2022
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1760 Å2
ΔGint-11 kcal/mol
Surface area6120 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: 11003.271 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 UUAGGUC


Mass: 2198.339 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
134isotropic42D 1H-13C HSQC aromatic
142isotropic13D HNCA
152isotropic13D HN(CA)CB
162isotropic13D CBCA(CO)NH
172isotropic13D HNCO
182isotropic33D HCc(CO)NH TOCSY
192isotropic33D hCC(CO)NH TOCSY
1101isotropic53D 1H-15N NOESY
1112isotropic53D 1H-13C NOESY aliphatic
1182isotropic53D 1H-13C NOESY aromatic
1173isotropic52D 1H-1H NOESY
1163isotropic52D 1H-1H TOCSY
1154isotropic32D F1fF2f 13C-filtered NOESY
1144isotropic13D F1eF3f 13C-filtered/edited NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 15N] hnRNP A1 RRM1, 1.0 mM RNA UUAGGUC, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21.0 mM [U-99% 13C; U-99% 15N] hnRNP A1 RRM1, 1.0 mM RNA UUAGGUC, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution31.0 mM [U-99% 15N] hnRNP A1 RRM1, 1.0 mM RNA UUAGGUC, 100% D2O15N_sample_D2O100% D2O
solution41.0 mM [U-99% 13C; U-99% 15N] hnRNP A1 RRM1, 1.0 mM RNA UUAGGUC, 100% D2O13C15N_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMhnRNP A1 RRM1[U-99% 15N]1
1.0 mMRNA UUAGGUCnatural abundance1
1.0 mMhnRNP A1 RRM1[U-99% 13C; U-99% 15N]2
1.0 mMRNA UUAGGUCnatural abundance2
1.0 mMhnRNP A1 RRM1[U-99% 15N]3
1.0 mMRNA UUAGGUCnatural abundance3
1.0 mMhnRNP A1 RRM1[U-99% 13C; U-99% 15N]4
1.0 mMRNA UUAGGUCnatural 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 III7003
Bruker AVANCE IIIBrukerAVANCE III7504
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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