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- PDB-4j50: Crystal Structure of an Expanded RNA CAG Repeat -

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Basic information

Entry
Database: PDB / ID: 4j50
TitleCrystal Structure of an Expanded RNA CAG Repeat
ComponentsRNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
KeywordsRNA / A form RNA / CAG repeat expansion / PolyQ / Gain of RNA Function / Huntingtin Disease / Spinal-Bulbar Muscular Atrophy / Dentatorubral-pallidoluysian atrophy / Spinocerebellar ataxia
Function / homologyPHOSPHATE ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPark, H. / Disney, M.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations.
Authors: Yildirim, I. / Park, H. / Disney, M.D. / Schatz, G.C.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(*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
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-8 kcal/mol
Surface area6490 Å2
MethodPISA
2
A: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
hetero molecules

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

A: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(*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)37,22212
Polymers36,6526
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9650 Å2
ΔGint-77 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.338, 46.338, 134.597
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-206-

HOH

41A-208-

HOH

51A-218-

HOH

61A-221-

HOH

71B-201-

HOH

81B-204-

HOH

91B-237-

HOH

101B-239-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B

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Components

#1: RNA chain RNA (5'-R(*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: vitro transcription / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15 mM Mg Acetate, 50 mM Na cacodylate, 1.7 M Am Sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97937 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2011
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 12996 / Num. obs: 13022 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.65→1.74 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→22.433 Å / SU ML: 0.1 / σ(F): 0.21 / Phase error: 16.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1797 608 4.94 %Random
Rwork0.1685 ---
obs0.169 12318 94.97 %-
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.182 Å2 / ksol: 0.459 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0277 Å2-0 Å2-0 Å2
2---0.0277 Å2-0 Å2
3---0.0555 Å2
Refinement stepCycle: LAST / Resolution: 1.65→22.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 10 112 930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004910
X-RAY DIFFRACTIONf_angle_d0.6971416
X-RAY DIFFRACTIONf_dihedral_angle_d13.863448
X-RAY DIFFRACTIONf_chiral_restr0.053188
X-RAY DIFFRACTIONf_plane_restr0.00538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A612X-RAY DIFFRACTIONPOSITIONAL
12B612X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6504-1.81640.1791450.1892701X-RAY DIFFRACTION88
1.8164-2.07910.20131520.16612934X-RAY DIFFRACTION95
2.0791-2.61880.19321560.16663017X-RAY DIFFRACTION98
2.6188-22.43490.16981550.1673058X-RAY DIFFRACTION99
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)
10.00480.0033-0.00650.0034-0.00720.00690.0113-0.17050.01530.31840.0527-0.2202-0.1870.2038-0.00030.4101-0.0008-0.03050.2306-0.00140.29962.937214.7626-15.2345
20.1516-0.21810.18360.7883-0.36550.26410.1851-0.24350.06370.23020.0656-0.0341-0.36680.32490.18530.3348-0.0660.00390.3374-0.06230.20396.87516.4091-7.134
30.00740.0101-0.01560.0104-0.02370.0563-0.0337-0.04640.03040.0270.0715-0.1087-0.05520.05610.0431.1032-0.43470.25471.0635-0.24110.229210.208818.02185.9077
40.3774-0.17790.190.2861-0.12890.11430.1727-0.018-0.0247-0.17210.1193-0.2007-0.48180.17070.02230.3227-0.00140.03890.18670.00710.23240.2319.835517.2695
50.00120.00220.00270.00650.00790.006-0.01360.31230.1124-0.18270.05640.0453-0.30460.0782-0.00020.2853-0.0713-0.00930.36570.02730.270711.31279.928915.2401
60.0034-0.0021-00.00840.01410.01450.12310.1447-0.1183-0.09080.1664-0.0619-0.22160.18840.00010.2619-0.03360.03580.26490.00380.21773.07125.46259.7978
70.061-0.0254-0.0660.0129-0.02190.47230.09730.07520.0947-0.05880.17460.1083-0.11160.06160.34051.2659-0.17420.27380.6994-0.02690.19637.089117.3927-3.3154
80.5017-0.14260.28710.1669-0.12120.19440.2102-0.14750.16-0.0080.08010.0404-0.36120.37970.02630.2115-0.05360.01690.2921-0.04010.22598.40535.1194-17.2638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:4)
2X-RAY DIFFRACTION2(chain A and resid 5:10)
3X-RAY DIFFRACTION3(chain A and resid 11:14)
4X-RAY DIFFRACTION4(chain A and resid 15:19)
5X-RAY DIFFRACTION5(chain B and resid 1:4)
6X-RAY DIFFRACTION6(chain B and resid 5:8)
7X-RAY DIFFRACTION7(chain B and resid 9:14)
8X-RAY DIFFRACTION8(chain B and resid 15:19)

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