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- PDB-2f8k: Sequence specific recognition of RNA hairpins by the SAM domain o... -

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Basic information

Entry
Database: PDB / ID: 2f8k
TitleSequence specific recognition of RNA hairpins by the SAM domain of Vts1
Components
  • 5'-R(*UP*AP*AP*UP*CP*UP*UP*UP*GP*AP*CP*AP*GP*AP*UP*U)-3'
  • Protein VTS1
KeywordsRNA BINDING PROTEIN/ RNA / VTS1-RNA complex / SAM domain / RNA BINDING PROTEIN- RNA COMPLEX
Function / homology
Function and homology information


flap-structured DNA binding / positive regulation of DNA metabolic process / nuclear-transcribed mRNA poly(A) tail shortening / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAviv, T. / Lin, Z. / Ben-Ari, G. / Smibert, C.A. / Sicheri, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.
Authors: Aviv, T. / Lin, Z. / Ben-Ari, G. / Smibert, C.A. / Sicheri, F.
History
DepositionDec 2, 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: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: 5'-R(*UP*AP*AP*UP*CP*UP*UP*UP*GP*AP*CP*AP*GP*AP*UP*U)-3'
A: Protein VTS1


Theoretical massNumber of molelcules
Total (without water)15,1252
Polymers15,1252
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.550, 44.530, 129.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 5045.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SRE23
#2: Protein Protein VTS1 / VTI1-2 suppressor protein 1


Mass: 10079.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VTS1 / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q08831
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.5 M Ammonium sulfate, 50 mM MES pH 5.5, 10 mM Magnesium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium sulfate11
2MES11
3Magnesium Acetate11
4H2O11
5Ammonium sulfate12
6MES12
7Magnesium Acetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→64.55 Å / Num. obs: 11366 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.057 / Net I/σ(I): 11.37
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 6.43 / Num. unique all: 1523 / Rsym value: 0.139 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2D3D

2d3d


Resolution: 2→64.55 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.102 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 789 6.9 %RANDOM
Rwork0.228 ---
all0.231 11388 --
obs0.23 11366 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.027 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms672 317 0 117 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221052
X-RAY DIFFRACTIONr_angle_refined_deg1.3192.3721495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.659587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.63623.57128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85515133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.707155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02669
X-RAY DIFFRACTIONr_nbd_refined0.1970.2482
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.211
X-RAY DIFFRACTIONr_mcbond_it0.4071.5439
X-RAY DIFFRACTIONr_mcangle_it0.7012692
X-RAY DIFFRACTIONr_scbond_it1.0553781
X-RAY DIFFRACTIONr_scangle_it1.5954.5802
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 54 -
Rwork0.367 743 -
obs-797 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.62420.77462.70532.23351.7924.96830.06810.0536-0.03360.06420.0722-0.10970.10060.0206-0.1403-0.16960.01770.0206-0.1432-0.0227-0.1122-0.91171.2516-8.7157
22.0831-1.92431.51074.0011-2.07015.5671-0.10610.46420.3536-0.05270.1561-0.351-0.610.3721-0.04990.0139-0.0122-0.0016-0.00960.0132-0.0677-0.56163.5713-29.5236
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AB440 - 5235 - 88
22BA0 - 151 - 16

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