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- PDB-1fnx: SOLUTION STRUCTURE OF THE HUC RBD1-RBD2 COMPLEXED WITH THE AU-RIC... -

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Basic information

Entry
Database: PDB / ID: 1fnx
TitleSOLUTION STRUCTURE OF THE HUC RBD1-RBD2 COMPLEXED WITH THE AU-RICH ELEMENT
Components
  • AU-RICH RNA ELEMENT
  • HU ANTIGEN C
Keywordsimmune system/RNA / RNA-binding domain / protein-RNA complex / immune system-RNA COMPLEX
Function / homology
Function and homology information


mRNA 3'-UTR AU-rich region binding / nervous system development / cell differentiation / ribonucleoprotein complex
Similarity search - Function
HuC, RNA recognition motif 3 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...HuC, RNA recognition motif 3 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / RNA recognition motif domain, eukaryote / RNA recognition motif / 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 / ELAV-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsInoue, M. / Hirao, M. / Kasashima, K. / Kim, I.-S. / Kawai, G. / Kigawa, T. / Sakamoto, H. / Muto, Y. / Yokoyama, S.
CitationJournal: To be Published / Year: 2000
Title: Solution structure of mouse HuC RNA-binding domains complexed with an AU-Rich element reveals determinants of neuronal differentiation
Authors: Inoue, M. / Hirao, M. / Kasashima, K. / Kim, I.-S. / Kawai, G. / Kigawa, T. / Sakamoto, H. / Muto, Y. / Yokoyama, S.
History
DepositionAug 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 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
R: AU-RICH RNA ELEMENT
H: HU ANTIGEN C


Theoretical massNumber of molelcules
Total (without water)22,2442
Polymers22,2442
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)21 / 200structures with the lowest energy. CONFORMER 21 IS THE MINIMIZED AVERAGE STRUCTURE OF CONFORMERS 1-20
RepresentativeModel #21conformer 21 is the minimized average structure of conformers 1-20

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Components

#1: RNA chain AU-RICH RNA ELEMENT


Mass: 3062.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA DECAMER
#2: Protein HU ANTIGEN C


Mass: 19180.775 Da / Num. of mol.: 1 / Fragment: THE FIRST AND THE SECOND RNA-BINDING DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q60900

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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
1323D 13C-separated NOESY
1433D 13C-separated NOESY
1543D 13C-separated NOESY
1653D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
120mM phosphate K buffer; 0.8mM RBD1-RBD2 U-15N,13C; 0.8mM ARE; 1mM DTT; 100 units/ml ribonuclease inhibitor90% H2O/10% D2O
220mM phosphate K buffer; 0.8mM RBD1-RBD2; 0.8mM ARE U-15N,13C; 1mM DTT; 100 units/ml ribonuclease inhibitor90% H2O/10% D2O
320mM phosphate K buffer; 0.8mM RBD1-RBD2; 0.8mM ARE U-15N,13C; 1mM DTT; 100 units/ml ribonuclease inhibitor100% D2O
420mM phosphate K buffer; 0.8mM RBD1-RBD2; 0.8mM ARE U-15N,13C-Adenosine; 1mM DTT; 100 units/ml ribonuclease inhibitor90% H2O/10% D2O
520mM phosphate K buffer; 0.8mM RBD1-RBD2; 0.8mM ARE U-15N,13C-Adenosine; 1mM DTT; 100 units/ml ribonuclease inhibitor100% D2O
Sample conditionsIonic strength: 20mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS0.9Brungerstructure solution
CNS0.9Brunger et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: conformer 21 is the minimized average structure of conformers 1-20
NMR ensembleConformer selection criteria: structures with the lowest energy. CONFORMER 21 IS THE MINIMIZED AVERAGE STRUCTURE OF CONFORMERS 1-20
Conformers calculated total number: 200 / Conformers submitted total number: 21

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