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- PDB-2mqp: Structural Investigation of hnRNP L bound to RNA -

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Basic information

Entry
Database: PDB / ID: 2mqp
TitleStructural Investigation of hnRNP L bound to RNA
Components
  • Protein Hnrnpl
  • RNA (5'-R(*AP*CP*AP*CP*AP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / Protein-RNA Complex / RRM / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Processing of Capped Intron-Containing Pre-mRNA / mRNA CDS binding / mRNA Splicing - Major Pathway / response to peptide / ribonucleoprotein granule / pronucleus / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / regulation of RNA splicing / pre-mRNA intronic binding ...Processing of Capped Intron-Containing Pre-mRNA / mRNA CDS binding / mRNA Splicing - Major Pathway / response to peptide / ribonucleoprotein granule / pronucleus / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / regulation of RNA splicing / pre-mRNA intronic binding / cellular response to amino acid starvation / mRNA 3'-UTR binding / positive regulation of translation / mRNA processing / circadian rhythm / transcription cis-regulatory region binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / mRNA binding / synapse / chromatin / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
hnRNP-L, RNA recognition motif 3 / hnRNP-L, RNA recognition motif 4 / hnRNP-L, RNA recognition motif 1 / hnRNP-L, RNA recognition motif 2 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RRM (RNA recognition motif) domain / RNA recognition motif ...hnRNP-L, RNA recognition motif 3 / hnRNP-L, RNA recognition motif 4 / hnRNP-L, RNA recognition motif 1 / hnRNP-L, RNA recognition motif 2 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP 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 L / Heterogeneous nuclear ribonucleoprotein L
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsBlatter, M. / Allain, F.
CitationJournal: To be Published
Title: Structural Investigation of hnRNP L bound to RNA
Authors: Blatter, M. / Allain, F.
History
DepositionJun 24, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: pdbx_database_related
Item: _pdbx_database_related.db_id / _pdbx_database_related.db_name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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
Revision 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: Protein Hnrnpl
B: RNA (5'-R(*AP*CP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)14,9382
Polymers14,9382
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 / 250structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein Hnrnpl


Mass: 13079.706 Da / Num. of mol.: 1 / Fragment: unp residues 174-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hnrnpl / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z3R2, UniProt: F1LQ48*PLUS
#2: RNA chain RNA (5'-R(*AP*CP*AP*CP*AP*C)-3')


Mass: 1858.205 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Second RNA Recognition Motif Domain of hnRNP L bound to ACACAC RNA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY aliphatic
1323D 1H-13C NOESY aromatic
1432D 1H-1H NOESY
1532D 1H-1H TOCSY
1643D F3-filtered-F2-edited NOESY
1742D F2-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-100% 15N] protein_1, 2 mM RNA (5'-R(*AP*CP*AP*CP*AP*C)-3'), 60 mM sodium chloride, 40 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-100% 13C; U-100% 15N] protein_1, 2 mM RNA (5'-R(*AP*CP*AP*CP*AP*C)-3'), 60 mM sodium chloride, 40 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
32 mM [U-100% 15N] protein_1, 2 mM protein_1, 60 mM sodium chloride, 40 mM sodium phosphate, 1 mM DTT, 100% D2O100% D2O
42 mM [U-100% 13C; U-100% 15N] protein_1, 2 mM RNA (5'-R(*AP*CP*AP*CP*AP*C)-3'), 60 mM sodium chloride, 40 mM sodium phosphate, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity_1-1[U-100% 15N]1
2 mMRNA (5'-R(*AP*CP*AP*CP*AP*C)-3')-21
60 mMsodium chloride-31
40 mMsodium phosphate-41
1 mMDTT-51
2 mMentity_1-6[U-100% 13C; U-100% 15N]2
2 mMRNA (5'-R(*AP*CP*AP*CP*AP*C)-3')-72
60 mMsodium chloride-82
40 mMsodium phosphate-92
1 mMDTT-102
2 mMentity_1-11[U-100% 15N]3
2 mMentity_1-123
60 mMsodium chloride-133
40 mMsodium phosphate-143
1 mMDTT-153
2 mMentity_1-16[U-100% 13C; U-100% 15N]4
2 mMRNA (5'-R(*AP*CP*AP*CP*AP*C)-3')-174
60 mMsodium chloride-184
40 mMsodium phosphate-194
1 mMDTT-204
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 310.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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