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- PDB-4yn6: Structural Insight reveals dynamics in repeating r(CAG) transcrip... -

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Basic information

Entry
Database: PDB / ID: 4yn6
TitleStructural Insight reveals dynamics in repeating r(CAG) transcript found in Huntington's disease (HD) and Spinocerebellar ataxias (SCAs)
ComponentsRNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
KeywordsRNA / Trinucleotide repeat / Huntington's disease (HD) / Spinocerebellar ataxias (SCAs)
Function / homologyPHOSPHATE ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.301 Å
AuthorsTawani, A. / Kumar, A.
CitationJournal: Plos One / Year: 2015
Title: Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs)
Authors: Tawani, A. / Kumar, A.
History
DepositionMar 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Data collection
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 2, 2015Group: Data collection
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4074
Polymers12,2172
Non-polymers1902
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-17 kcal/mol
Surface area6700 Å2
Unit cell
Length a, b, c (Å)46.074, 46.074, 133.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-101-

PO4

21B-101-

PO4

31A-212-

HOH

41A-214-

HOH

51A-221-

HOH

61B-211-

HOH

71B-217-

HOH

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Components

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


Mass: 6108.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50mM Tris HCl, 25mM Magnesium Sulphate and 1.8M Ammonium Sulfate
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Feb 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 7642 / % possible obs: 99.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootphasing
RefinementResolution: 2.301→44.401 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 210 4.51 %RANDOM
Rwork0.2168 ---
obs0.2189 4657 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→44.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 814 10 54 878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005916
X-RAY DIFFRACTIONf_angle_d1.3871424
X-RAY DIFFRACTIONf_dihedral_angle_d15.266450
X-RAY DIFFRACTIONf_chiral_restr0.159190
X-RAY DIFFRACTIONf_plane_restr0.00638
LS refinement shellResolution: 1.95→2.3006 Å
RfactorNum. reflection% reflection
Rfree0.2607 210 -
Rwork0.2168 4447 -
obs--99 %

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