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- PDB-1fje: SOLUTION STRUCTURE OF NUCLEOLIN RBD12 IN COMPLEX WITH SNRE RNA -

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Basic information

Entry
Database: PDB / ID: 1fje
TitleSOLUTION STRUCTURE OF NUCLEOLIN RBD12 IN COMPLEX WITH SNRE RNA
Components
  • NUCLEOLIN RBD12
  • SNRE RNA
KeywordsSTRUCTURAL PROTEIN/RNA / RNP / RBD / RRM / RNA binding domain / RNA-protein complex / Nucleolus / STRUCTURAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


positive regulation of mRNA splicing, via spliceosome / telomeric DNA binding / spliceosomal complex / 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
RNA / RNA (> 10) / Nucleolin
Similarity search - Component
Biological speciesMesocricetus auratus (golden hamster)
MethodSOLUTION NMR / simulated annealing using XPLOR 3.841
AuthorsAllain, F.H.T. / Bouvet, P. / Dieckmann, T. / Feigon, J.
Citation
Journal: EMBO J. / Year: 2000
Title: Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin.
Authors: Allain, F.H. / Bouvet, P. / Dieckmann, T. / Feigon, J.
#1: Journal: 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.T. / Gilbert, D.E. / Bouvet, P. / Feigon, J.
History
DepositionAug 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2001Provider: 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: SNRE RNA
B: NUCLEOLIN RBD12


Theoretical massNumber of molelcules
Total (without water)26,4612
Polymers26,4612
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)19 / 40all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: RNA chain SNRE RNA


Mass: 7095.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription by T7 RNA polymerase
#2: Protein NUCLEOLIN RBD12 / PROTEIN C23


Mass: 19365.744 Da / Num. of mol.: 1 / Fragment: TWO N-TERMINAL RBD DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Plasmid: PET15-B / 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
12113C-12C filtered 3D
1323D 15N-separated NOESY
1432D NOESY
2532D NOESY
1643D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N,13C nucleolin RBD12 in complex with unlabeled RNA90% H2O/10% D2O
21mM U-15N nucleolin RBD12 in complex with unlabeled RNA90% H2O/10% D2O
31mM U-15N nucleolin RBD12 in complex with unlabeled RNA100% D2O
41mM U-15N-13C RNA in complex with U-15N nucleolin RBD12100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 6.2 ambient 303 K
2150 6.2 ambient 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.841BRUNGERrefinement
X-PLOR3.841BRUNGERstructure solution
RefinementMethod: simulated annealing using XPLOR 3.841 / Software ordinal: 1
Details: structures are based on 3246 constraints, 3010 are NOE-derived including 150 intermolecular
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 40 / Conformers submitted total number: 19

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