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- PDB-2dnp: Solution structure of RNA binding domain 2 in RNA-binding protein 14 -

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Basic information

Entry
Database: PDB / ID: 2dnp
TitleSolution structure of RNA binding domain 2 in RNA-binding protein 14
ComponentsRNA-binding protein 14
KeywordsTRANSCRIPTION / RRM domain / RBD / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of response to DNA integrity checkpoint signaling / centriole assembly / RUNX2 regulates bone development / negative regulation of centriole replication / splicing factor binding / activation of innate immune response / gastrulation / response to hormone / transcription initiation-coupled chromatin remodeling / nuclear receptor coactivator activity ...regulation of response to DNA integrity checkpoint signaling / centriole assembly / RUNX2 regulates bone development / negative regulation of centriole replication / splicing factor binding / activation of innate immune response / gastrulation / response to hormone / transcription initiation-coupled chromatin remodeling / nuclear receptor coactivator activity / mRNA splicing, via spliceosome / transcription regulator complex / nuclear speck / ribonucleoprotein complex / innate immune response / mRNA binding / nucleolus / apoptotic process / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
RBM14, RNA recognition motif 1 / RBM14, RNA recognition motif 2 / : / 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 ...RBM14, RNA recognition motif 1 / RBM14, RNA recognition motif 2 / : / 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-binding protein 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsKusuhara, M. / 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 RNA binding domain 2 in RNA-binding protein 14
Authors: Kusuhara, M. / Tsuda, K. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 14


Theoretical massNumber of molelcules
Total (without water)9,6481
Polymers9,6481
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 RNA-binding protein 14 / RNA-binding motif protein 14 / RRM-containing coactivator activator/modulator / Synaptotagmin- ...RNA-binding motif protein 14 / RRM-containing coactivator activator/modulator / Synaptotagmin-interacting protein / SYT-interacting protein


Mass: 9647.904 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: RBM14 / Plasmid: P051121-02 / Production host: Cell free synthesis / References: UniProt: Q96PK6

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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: 0.66mM 13C-15N PROTEIN, 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / 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
KUJIRA0.9736Kobayashi,Ndata analysis
CYANA2.0.17Guntert,Pstructure solution
CYANA2.0.17Guntert,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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