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- PDB-2kxh: Solution structure of the first two RRM domains of FIR in the com... -

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Basic information

Entry
Database: PDB / ID: 2kxh
TitleSolution structure of the first two RRM domains of FIR in the complex with FBP Nbox peptide
Components
  • Poly(U)-binding-splicing factor PUF60
  • peptide of Far upstream element-binding protein 1
KeywordsPROTEIN BINDING / RRM / FIR / FBP / protein-protein complex
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / mRNA splice site recognition / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / cell junction / single-stranded DNA binding / regulation of gene expression / cadherin binding ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / cell junction / single-stranded DNA binding / regulation of gene expression / cadherin binding / mRNA binding / apoptotic process / positive regulation of gene expression / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / : / : / : / Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) ...: / : / : / : / Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / RNA recognition motif domain, eukaryote / RNA recognition motif / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / 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 / K Homology domain / K homology RNA-binding domain / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Far upstream element-binding protein 1 / Poly(U)-binding-splicing factor PUF60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsCukier, C.D. / Ramos, A. / Hollingworth, D. / Diaz-Moreno, I. / Kelly, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Molecular basis of FIR-mediated c-myc transcriptional control.
Authors: Cukier, C.D. / Hollingworth, D. / Martin, S.R. / Kelly, G. / Diaz-Moreno, I. / Ramos, A.
History
DepositionMay 5, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 18, 2019Group: Data collection / Database references
Category: citation / pdbx_nmr_software ...citation / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(U)-binding-splicing factor PUF60
B: peptide of Far upstream element-binding protein 1


Theoretical massNumber of molelcules
Total (without water)25,0852
Polymers25,0852
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Poly(U)-binding-splicing factor PUF60 / 60 kDa poly(U)-binding-splicing factor / FUSE-binding protein-interacting repressor / FBP- ...60 kDa poly(U)-binding-splicing factor / FUSE-binding protein-interacting repressor / FBP-interacting repressor / Siah-binding protein 1 / Siah-BP1 / Ro-binding protein 1 / RoBP1


Mass: 21927.018 Da / Num. of mol.: 1 / Fragment: UNP residues 119-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UHX1
#2: Protein/peptide peptide of Far upstream element-binding protein 1 / FUSE-binding protein 1 / FBP / DNA helicase V / hDH V


Mass: 3157.519 Da / Num. of mol.: 1 / Fragment: UNP residues 27-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96AE4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HNCA
1233D (H)CCH-TOCSY
2333D (H)CCH-TOCSY
1443D 13C rejected 1H-13C NOESY
1513D 1H-15N NOESY
1643D 1H-13C NOESY without 13C decoupling during the indirectly acquired proton dimension
1733D 1H-13C NOESY without 13C decoupling during the indirectly acquired proton dimension
2833D 1H-13C NOESY without 13C decoupling during the indirectly acquired proton dimension
1943D 1H-13C NOESY
11023D 1H-13C NOESY
11133D 1H-13C NOESY
21233D 1H-13C NOESY
11343D 1H-13C NOESY optmised for aromatics

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-15N] protein_1-1, 10 mM TRIS-HCl pH 8.0-2, 50 mM sodium chloride-3, 2 mM TCEP-4, 1.25 mM protein_2-5, 90% H2O/10% D2O90% H2O/10% D2O
2mM [U-13C; U-15N] protein_1-6, 10 mM TRIS-HCl pH 8.0-7, 50 mM sodium chloride-8, 2 mM TCEP-9, mM protein_2-10, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM [U-13C; U-15N] protein_2-11, 10 mM TRIS-HCl pH 8.0-12, 50 mM sodium chloride-13, 2 mM TCEP-14, mM protein_1-15, 100% D2O100% D2O
4mM [U-13C; U-15N] protein_1-16, 10 mM TRIS-HCl pH 8.0-17, 50 mM sodium chloride-18, 2 mM TCEP-19, mM protein_2-20, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.6 mMprotein_1-1[U-15N]1
10 mMTRIS-HCl pH 8.0-21
50 mMsodium chloride-31
2 mMTCEP-41
1.25 mMprotein_2-51
mMprotein_1-6[U-13C; U-15N]0.3-0.52
10 mMTRIS-HCl pH 8.0-72
50 mMsodium chloride-82
2 mMTCEP-92
mMprotein_2-100.6-1.42
0.3 mMprotein_2-11[U-13C; U-15N]3
10 mMTRIS-HCl pH 8.0-123
50 mMsodium chloride-133
2 mMTCEP-143
mMprotein_1-150.6-0.73
mMprotein_1-16[U-13C; U-15N]0.3-0.54
10 mMTRIS-HCl pH 8.0-174
50 mMsodium chloride-184
2 mMTCEP-194
mMprotein_2-200.6-1.44
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.06 8.0 ambient 310 K
20.06 8.0 ambient 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
XEASYBartels et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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