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- PDB-2err: NMR Structure of the RNA Binding Domain of Human Fox-1 in Complex... -

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Basic information

Entry
Database: PDB / ID: 2err
TitleNMR Structure of the RNA Binding Domain of Human Fox-1 in Complex with UGCAUGU
Components
  • Ataxin-2-binding protein 1
  • UGCAUGU
KeywordsRNA BINDING PROTEIN / PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


regulation of skeletal muscle cell differentiation / RNA transport / nuclear stress granule / MECP2 regulates transcription factors / regulation of alternative mRNA splicing, via spliceosome / neuromuscular process controlling balance / RNA splicing / mRNA 3'-UTR binding / trans-Golgi network / mRNA processing ...regulation of skeletal muscle cell differentiation / RNA transport / nuclear stress granule / MECP2 regulates transcription factors / regulation of alternative mRNA splicing, via spliceosome / neuromuscular process controlling balance / RNA splicing / mRNA 3'-UTR binding / trans-Golgi network / mRNA processing / cytoplasmic stress granule / nervous system development / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / RNA binding protein Fox-1 / Fox-1 C-terminal domain / Calcitonin gene-related peptide regulator C terminal / FOX1, 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 protein Fox-1 / Fox-1 C-terminal domain / Calcitonin gene-related peptide regulator C terminal / FOX1, 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 / RNA binding protein fox-1 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAllain, F.H. / Auweter, S.D.
CitationJournal: Embo J. / Year: 2006
Title: Molecular basis of RNA recognition by the human alternative splicing factor Fox-1.
Authors: Auweter, S.D. / Fasan, R. / Reymond, L. / Underwood, J.G. / Black, D.L. / Pitsch, S. / Allain, F.H.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: UGCAUGU
A: Ataxin-2-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,5982
Polymers14,5982
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)30 / 30all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: RNA chain UGCAUGU


Mass: 2198.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#2: Protein Ataxin-2-binding protein 1


Mass: 12399.978 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: A2BP1, A2BP / Plasmid: pET28a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NWB1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1243D 13C-separated NOESY
1313D 15N-separated NOESY
142HNCA
152CBCA(CO)NH
162HN(CO)CA
174(H)CCH-TOCSY
1852D F1,F2-edited NOESY
1952D F1-edited, F2-fitered NOESY
11062D F1-edited, F2-fitered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Fox-1 15N; 1mM UGCAUGU; 20mM sodium phoshphate; 30mM NaCl90% H2O/10% D2O
21mM Fox-1 15N, 13C; 1mM UGUAUGU; 20mM sodium phoshphate; 30mM NaCl90% H2O/10% D2O
31mM Fox-1 15N; 1mM UGCAUGU; 20mM sodium phoshphate; 30mM NaCl100% D2O
41mM Fox-1 15N, 13C; 1mM UGCAUGU; 20mM sodium phoshphate; 30mM NaCl100% D2O
51mM Fox-1 15N; 1mM UGCAUGU, sugars of U1, C3, U5 13C; 20mM sodium phoshphate; 30mM NaCl100% D2O
61mM Fox-1 15N; 1mM UGCAUGU, sugars of G2, A4, G6, U7 13C; 20mM sodium phoshphate; 30mM NaCl100% D2O
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 313 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 DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Peter Guentertstructure solution
Amber7David A. Caserefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1460 NOE-derived distance constraints, 29 hydrogen bond constraints and 6 torsion angle constraints. 149 and 119 of the NOE constraints are ...Details: The structures are based on a total of 1460 NOE-derived distance constraints, 29 hydrogen bond constraints and 6 torsion angle constraints. 149 and 119 of the NOE constraints are intermolecular and intra-RNA, respectively.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 30 / Conformers submitted total number: 30

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