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- PDB-1fj7: SOLUTION STRUCTURE OF NUCLEOLIN RBD1 -

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Basic information

Entry
Database: PDB / ID: 1fj7
TitleSOLUTION STRUCTURE OF NUCLEOLIN RBD1
ComponentsNUCLEOLIN RBD1
KeywordsSTRUCTURAL PROTEIN / RNP / RBD / RRM / RNA binding domain / Nucleolus
Function / homology
Function and homology information


telomeric DNA binding / ribonucleoprotein complex / nucleolus / RNA binding / cytoplasm
Similarity search - Function
Nucleolin, RNA recognition motif 1 / Nucleolin, RNA recognition motif 2 / Nucleolin, RNA recognition motif 3 / Nucleolin, RNA recognition motif 4 / 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 ...Nucleolin, RNA recognition motif 1 / Nucleolin, RNA recognition motif 2 / Nucleolin, RNA recognition motif 3 / Nucleolin, RNA recognition motif 4 / 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
Biological speciesMesocricetus auratus (golden hamster)
MethodSOLUTION NMR / simulated annealing using X-PLOR 3.841
AuthorsAllain, F.H.-T. / Gilbert, D.E. / Bouvet, P. / Feigon, J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Solution structure of the two N-terminal RNA-binding domains of nucleolin and NMR study of the interaction with its RNA target.
Authors: Allain, F.H. / Gilbert, D.E. / Bouvet, P. / Feigon, J.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2000Provider: 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
A: NUCLEOLIN RBD1


Theoretical massNumber of molelcules
Total (without water)11,0291
Polymers11,0291
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)34 / 50all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein NUCLEOLIN RBD1 / PROTEIN C23


Mass: 11029.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Plasmid: BL21(DE3)PLYSS / Production host: Escherichia coli (E. coli) / References: UniProt: P08199

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1mM U-15N,13C; 50mM potassium phosphate buffer; 100 mM KCl, 5mM deuterated DTT, pH 6.2
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150 / pH: 6.2 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.841Brungerrefinement
X-PLOR3.841Brungerstructure solution
DYANA1Guntertstructure solution
RefinementMethod: simulated annealing using X-PLOR 3.841 / Software ordinal: 1
Details: structures are based on 1391 restraints, 1335 are NOE-derived and 56 are from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 50 / Conformers submitted total number: 34

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