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- PDB-2lyv: Solution structure of the two RRM domains of hnRNP A1 (UP1) using... -

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Basic information

Entry
Database: PDB / ID: 2lyv
TitleSolution structure of the two RRM domains of hnRNP A1 (UP1) using segmental isotope labeling
ComponentsHeterogeneous nuclear ribonucleoprotein A1
KeywordsSPLICING / TRANSPORT PROTEIN / UP1 / hnRNP A1
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
Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBarraud, P. / Allain, F.H.-T.
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling: how the relative orientation between RRMs influences the nucleic acid binding topology.
Authors: Barraud, P. / Allain, F.H.
History
DepositionSep 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)22,2861
Polymers22,2861
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 lowest energy
RepresentativeModel #1lowest energy

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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: 22285.990 Da / Num. of mol.: 1 / Fragment: RRM domains 1 and 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1, HNRPA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL / References: UniProt: P09651

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1242D 1H-13C HSQC aliphatic
1342D 1H-13C HSQC aromatic
1443D HNCA
1543D HN(CA)CB
1643D CBCA(CO)NH
1743D HNCO
1843D HN(CA)CO
1943D H(CCO)NH
11043D C(CO)NH
11123D 1H-15N NOESY
11243D 1H-13C NOESY aromatic
11343D 1H-13C NOESY aliphatic
11432D 1H-1H NOESY
11532D 1H-1H TOCSY
11622D 1H-15N IPAP HSQC
11722D long-range 1H-15N HSQC
11813D 13C F1-edited F3-filtered NOESY-HSQC
11922D 1H-15N IPAP HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM RRM1[U-13C, U-15N]-RRM2[natural abundance] UP1, 10 mM sodium phosphate, 1 mM DTT, 100% D2O100% D2O
20.8-1.2 mM [U-15N] UP1, 10 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.8-1.2 mM [U-15N] UP1, 10 mM sodium phosphate, 1 mM DTT, 100% D2O100% D2O
40.8-1.2 mM [U-13C; U-15N] UP1, 10 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
1.0 mMUP1-1RRM1[U-13C, U-15N]-RRM2[natural abundance]1
10 mMsodium phosphate-21
1 mMDTT-31
mMUP1-4[U-15N]0.8-1.22
10 mMsodium phosphate-52
1 mMDTT-62
mMUP1-7[U-15N]0.8-1.23
10 mMsodium phosphate-83
1 mMDTT-93
mMUP1-10[U-13C; U-15N]0.8-1.24
10 mMsodium phosphate-114
1 mMDTT-124
Sample conditionsIonic strength: 10 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE7504
Bruker AvanceBrukerAVANCE9005

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
CYANA3Guntertstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOStalos+Cornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 5354 / NOE intraresidue total count: 1108 / NOE long range total count: 1870 / NOE medium range total count: 1015 / NOE sequential total count: 1361 / Hydrogen bond constraints total count: 2 / Protein phi angle constraints total count: 168 / Protein psi angle constraints total count: 168
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.5 ° / Maximum upper distance constraint violation: 0.27 Å
NMR ensemble rmsDistance rms dev: 0.04 Å

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