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- PDB-2b6g: RNA recognition by the Vts1 SAM domain -

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Basic information

Entry
Database: PDB / ID: 2b6g
TitleRNA recognition by the Vts1 SAM domain
Components
  • 5'-R(*GP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*C)-3'
  • Vts1p
KeywordsRNA BINDING PROTEIN / alpha-helix / pentaloop / hairpin
Function / homology
Function and homology information


flap-structured DNA binding / nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of DNA metabolic process / nuclear-transcribed mRNA catabolic process / P-body / protein transport / nucleotide binding / mRNA binding / RNA binding / nucleus / cytosol
Similarity search - Function
VTS1, SAM domain / : / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA-binding protein VTS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsDonaldson, L.W. / Johnson, P.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: RNA recognition by the Vts1p SAM domain
Authors: Johnson, P.E. / Donaldson, L.W.
History
DepositionOct 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 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_spectrometer ...database_2 / 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_spectrometer.model / _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
B: 5'-R(*GP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*C)-3'
A: Vts1p


Theoretical massNumber of molelcules
Total (without water)19,1832
Polymers19,1832
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)1 / -structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6086.633 Da / Num. of mol.: 1 / Fragment: Smaug Recognition Element / Source method: obtained synthetically
Details: RNA was produced by T7 polymerase based in vitro transcription
#2: Protein Vts1p


Mass: 13096.857 Da / Num. of mol.: 1 / Fragment: SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Vts1p / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 6324935, UniProt: Q08831*PLUS

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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
1412D 12C-filtered 13C-edited NOESY

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Sample preparation

DetailsContents: 0.2-0.8 mM U-15N,13C; 20 mM sodium phosphate buffer, pH 7.8, 150 mM sodium chloride, 0.02 % sodium azide
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 7.8 / Pressure: ambient / Temperature: 293 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 AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guentertstructure solution
XPLOR-NIH2.11.0Schweitersstructure solution
XPLOR-NIH2.11.0Schweitersrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Protein NOE restraints were calibrated from peak volumes to distances ranging from 1.8-5.0 using the CANDID module of CYANA v2.1. Initially, 100 structures were calculated with XPLOR-NIH v2. ...Details: Protein NOE restraints were calibrated from peak volumes to distances ranging from 1.8-5.0 using the CANDID module of CYANA v2.1. Initially, 100 structures were calculated with XPLOR-NIH v2.11.0 starting from a partially docked protein-RNA complex. A simulated annealing approach with internal torsion angle dynamics, delphic database potentials and RNA planarity restraints was used. From the initial ensemble of structures, 20 were selected based upon low energy, no NOE violations > 0.5 angstroms and no dihedral angle violations > 5 degrees. Restraints used for the structure calculation: 882 intraresidue protein-protein NOE, 435 sequential protein-protein NOE, 335 medium range protein-protein NOE, 263 long range protein-protein NOE, 80 protein hydrogen bonds, 60 RNA-RNA NOE, 23 protein-RNA NOE, 140 protein dihedral angle, 93 RNA dihedral angle.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers submitted total number: 1

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