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- PDB-2dh9: Solution structure of the C-terminal RNA binding domain in Hetero... -

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Basic information

Entry
Database: PDB / ID: 2dh9
TitleSolution structure of the C-terminal RNA binding domain in Heterogeneous nuclear ribonucleoprotein M
ComponentsHeterogeneous nuclear ribonucleoprotein M
KeywordsRNA BINDING PROTEIN / RRM domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / paraspeckles / FGFR2 alternative splicing / Processing of Capped Intron-Containing Pre-mRNA / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / nuclear matrix / collagen-containing extracellular matrix ...alternative mRNA splicing, via spliceosome / paraspeckles / FGFR2 alternative splicing / Processing of Capped Intron-Containing Pre-mRNA / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / nuclear matrix / collagen-containing extracellular matrix / protein domain specific binding / mRNA binding / synapse / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
Similarity search - Function
HnRNP M, nuclear localisation signal / hnRNPM, RNA recognition motif 3 / HnRNP M nuclear localisation signal / : / 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 M, nuclear localisation signal / hnRNPM, RNA recognition motif 3 / HnRNP M nuclear localisation signal / : / 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 M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics,restrained molecular dynamics
AuthorsOchi, T. / Tsuda, K. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the C-terminal RNA binding domain in Heterogeneous nuclear ribonucleoprotein M
Authors: Ochi, T. / Tsuda, K. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMar 23, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein M


Theoretical massNumber of molelcules
Total (without water)9,7791
Polymers9,7791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein M / hnRNP M


Mass: 9779.211 Da / Num. of mol.: 1 / Fragment: RNA recognition motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: HNRPM / Plasmid: P050711-05 / Production host: Cell free synthesis / References: UniProt: P52272

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 20mM d-Tris-HCl(pH 7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio,Fprocessing
NMRView5.0.4Johnson,B.Adata analysis
KUJIRA0.932Kobayashi,Ndata analysis
CYANA2Guntert,Pstructure solution
CYANA2Guntert,Prefinement
RefinementMethod: torsion angle dynamics,restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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