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- PDB-1k1g: STRUCTURAL BASIS FOR RECOGNITION OF THE INTRON BRANCH SITE RNA BY... -

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Basic information

Entry
Database: PDB / ID: 1k1g
TitleSTRUCTURAL BASIS FOR RECOGNITION OF THE INTRON BRANCH SITE RNA BY SPLICING FACTOR 1
Components
  • 5'-R(*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*A)-3'
  • SF1-Bo isoform
KeywordsGENE REGULATION/RNA / Splicing / branch point sequence / protein/RNA recognition / complex E / KH domain / QUA2 homology / STAR proteins / GENE REGULATION-RNA COMPLEX
Function / homology
Function and homology information


nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / mRNA Splicing - Major Pathway / negative regulation of smooth muscle cell proliferation ...nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / mRNA Splicing - Major Pathway / negative regulation of smooth muscle cell proliferation / spliceosomal complex / mRNA splicing, via spliceosome / transcription corepressor activity / nuclear body / ribosome / mRNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Splicing factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics, simulated annealing
AuthorsLiu, Z. / Luyten, I. / Bottomley, M.J. / Messias, A.C. / Houngninou-Molango, S. / Sprangers, R. / Zanier, K. / Kramer, A. / Sattler, M.
CitationJournal: Science / Year: 2001
Title: Structural basis for recognition of the intron branch site RNA by splicing factor 1.
Authors: Liu, Z. / Luyten, I. / Bottomley, M.J. / Messias, A.C. / Houngninou-Molango, S. / Sprangers, R. / Zanier, K. / Kramer, A. / Sattler, M.
History
DepositionSep 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*A)-3'
A: SF1-Bo isoform


Theoretical massNumber of molelcules
Total (without water)18,1622
Polymers18,1622
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)10 / 10010 lowest energy structures consistent with experimental distance and dihedral angle restraints
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*A)-3'


Mass: 3459.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Yeast and mammalian consensus BPS sequence
#2: Protein SF1-Bo isoform / Splicing Factor 1


Mass: 14702.896 Da / Num. of mol.: 1 / Fragment: Residues 133-260, KH-QUA2 region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: modified pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q15637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
1223D 13C/15N edited/filtered NOESY
1333D 15N-separated NOESY
NMR detailsText: Backbone and side chain 1H, 15N and 13C resonances were assigned using standard triple resonance experiments. Distance restraints were derived from 13C- and 15N-edited 3D NOESY experiments. ...Text: Backbone and side chain 1H, 15N and 13C resonances were assigned using standard triple resonance experiments. Distance restraints were derived from 13C- and 15N-edited 3D NOESY experiments. Assignments for the RNA were obtained from 2D isotope-filtered experiments. Intermolecular distance restraints were measured in 3D 13C-edited/filtered experiments. Dihedral angle restraints for the backbone angle phi were derived from 3J(HN,Ha) coupling constants measured in an HNHA-J experiment, additional phi/psi restraints were derived from TALOS. Hydrogen bond restraints for secondary structure elements in the protein were defined from slowly exchanging amide protons, identified after exchange of the H2O buffer to D2O.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N,13C SF1 KH-QUA2/unlabeled BPS in 20 mM phosphate buffer NA pH 6.5, 50 mM NaCl, 2 mM DTT90% H2O/10% D2O
21 mM U-15N,13C SF1 KH-QUA2/unlabeled BPS in 20 mM phosphate buffer NA pH 6.5, 50 mM NaCl, 2 mM DTT100% D2O
31 mM U-15N SF1 KH-QUA2/unlabeled BPS in 20 mM phosphate buffer NA pH 6.5, 50 mM NaCl, 2 mM DTT90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 6.5 ambient 295 K
250 mM NaCl 6.5 ambient 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe1.8F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, & A. Baxprocessing
XEASY1.2Ch. Bartels, T.-H. Xia, M. Billeter, P. Gntert and K. Wthrichdata analysis
ARIA/CNS1J. Linge, M. Nilgesstructure solution
ARIA/CNS1J. Linge, M. Nilgesrefinement
RefinementMethod: restrained molecular dynamics, simulated annealing / Software ordinal: 1
Details: STRUCTURES WERE CALCULATED WITH A MIXED TORSION AND CARTESIAN ANGLE DYNAMICS PROTOCOL USING ARIA/CNS. A REDUCED RELAXATION MATRIX APPROACH WAS USED FOR THE NOE CALIBRATION. THE STRUCTURES ...Details: STRUCTURES WERE CALCULATED WITH A MIXED TORSION AND CARTESIAN ANGLE DYNAMICS PROTOCOL USING ARIA/CNS. A REDUCED RELAXATION MATRIX APPROACH WAS USED FOR THE NOE CALIBRATION. THE STRUCTURES ARE CURRENTLY BEING REFINED USING RESIDUAL DIPOLAR COUPLINGS AND WILL BE UPDATED IN THE FUTURE.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 10 lowest energy structures consistent with experimental distance and dihedral angle restraints
Conformers calculated total number: 100 / Conformers submitted total number: 10

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