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- PDB-7u3r: [2T7+10] Self-assembling tensegrity triangle with two turns of DN... -

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Basic information

Entry
Database: PDB / ID: 7u3r
Title[2T7+10] Self-assembling tensegrity triangle with two turns of DNA and the sticky end attachment of a one-turn linker per axis, with R3 symmetry
Components
  • DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(*GP*AP*TP*GP*CP*TP*GP*AP*GP*T)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*GP*T)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*A)-3')
KeywordsDNA / Tensegrity triangle / self-assembling crystal
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.27 Å
AuthorsWoloszyn, K. / Vecchioni, S. / Lu, B. / Seeman, N.C. / Sha, R. / Ohayon, Y.P.
Funding support United States, France, 5items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141912596 United States
Department of Energy (DOE, United States)DE-SC0007991 United States
National Science Foundation (NSF, United States)2106790 United States
Human Frontier Science Program (HFSP)RPG0010/2017 France
National Science Foundation (NSF, United States)DMR-1420073 United States
CitationJournal: Adv Mater / Year: 2022
Title: Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants.
Authors: Woloszyn, K. / Vecchioni, S. / Ohayon, Y.P. / Lu, B. / Ma, Y. / Huang, Q. / Zhu, E. / Chernovolenko, D. / Markus, T. / Jonoska, N. / Mao, C. / Seeman, N.C. / Sha, R.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
Y: DNA (5'-D(*GP*AP*TP*GP*CP*TP*GP*AP*GP*T)-3')
X: DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*T)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
E: DNA (5'-D(P*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,8417
Polymers18,8417
Non-polymers00
Water00
1
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
Y: DNA (5'-D(*GP*AP*TP*GP*CP*TP*GP*AP*GP*T)-3')
X: DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*T)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
E: DNA (5'-D(P*AP*CP*A)-3')

C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
Y: DNA (5'-D(*GP*AP*TP*GP*CP*TP*GP*AP*GP*T)-3')
X: DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*T)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
E: DNA (5'-D(P*AP*CP*A)-3')

C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
Y: DNA (5'-D(*GP*AP*TP*GP*CP*TP*GP*AP*GP*T)-3')
X: DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*T)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
E: DNA (5'-D(P*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)56,52421
Polymers56,52421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)157.548, 157.548, 133.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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DNA chain , 7 types, 7 molecules CAYXBDE

#1: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2432.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6417.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*AP*TP*GP*CP*TP*GP*AP*GP*T)-3')


Mass: 3100.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*A)-3')


Mass: 3029.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*CP*CP*GP*T)-3')


Mass: 1166.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (5'-D(P*AP*CP*A)-3')


Mass: 870.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has ligand of interestN

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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: 16.92 Å3/Da / Density % sol: 92.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 120 mM Tris, 60 mM acetic acid, 6 mM EDTA, 150 mM ammonium sulfate, 37.5 mM magnesium sulfate
Temp details: 338K to 293K at 0.4K/hr, 293K to 277K at 0.1K/hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00743 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 6.27→95.41 Å / Num. obs: 1834 / % possible obs: 85 % / Redundancy: 10.9 % / Biso Wilson estimate: 465.58 Å2 / CC1/2: 1 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID% possible all
6.27-7.1352030.089151.5
14.912-95.412020.9991100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GBI

3gbi


Resolution: 6.27→36.41 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.4179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1872 116 6.46 %
Rwork0.1179 1679 -
obs0.1209 1795 66.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 663.02 Å2
Refinement stepCycle: LAST / Resolution: 6.27→36.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1201 61 0 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741410
X-RAY DIFFRACTIONf_angle_d1.00362161
X-RAY DIFFRACTIONf_chiral_restr0.0661245
X-RAY DIFFRACTIONf_plane_restr0.004562
X-RAY DIFFRACTIONf_dihedral_angle_d41.0837596
LS refinement shellResolution: 6.27→36.41 Å
RfactorNum. reflection% reflection
Rfree0.1872 116 -
Rwork0.1179 1679 -
obs--66.58 %
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)
17.45287672267-5.677430654180.6023575540634.97880399492-0.41298697861-0.1408993449288.205260920488.28131378164-3.79483607639-8.541925746375.07121245161-0.2238875807010.996367667897.029881522380.4432568351876.4867198489-0.694692067932-0.878335944747.31582697695-3.531558628127.007067020824.77466671820.512655692558-28.7562491148
27.073411232351.87055994426-5.00424373351-0.5972087487931.991284953174.043896507874.60422449661-1.25851514571-2.63772948072-3.490032892411.773760354599.21495053741-3.07663979301-0.269194142628-2.799312507825.92044985729-0.929534637218-2.109279864884.825415935830.4334434070317.492993140835.9841499416413.889260012-13.2647143208
30.1497224415840.882909779433-1.121506707552.226724563281.866820132667.33953718136-7.118326729390.104196297267-0.6955407800365.33905133108-8.96978393338-6.4527322202-1.848937077538.063185176250.2769542633164.883896033293.41097194026-0.021359292653314.8318956637-8.7490278001814.397644572746.2364041523-5.0077719081-35.9168111015
41.85652030835-0.3453060523412.59535783330.0741874526653-0.4390018210133.8216021014-3.23852572837-6.60213344953-1.421847146553.780809583613.407134759646.456931225-4.639801896752.186326089950.005824793315634.39429059844-1.138180544682.640250791095.97818715867-2.236498287039.4584601284458.1536159738-9.7119880551-45.8591612764
53.490158890073.21370185939-4.492915557273.28925346144-4.522707659976.19702752129-1.16283053885-8.002823866811.14683860257-6.517047776170.68390187286912.9383621428-4.80817891338-5.59486804626-3.569600061668.645692869850.8889465749470.56557643217310.6819448581-1.529811961398.1777645547545.6573634905-7.63582603241-32.4448326686
61.983805683757.59511855624-4.565118162053.84172363665-1.866839626442.19287706897-4.96600342432.22592675364-4.38866858091-4.14052613251-2.69136386991.43701550721-5.32996795005-0.9396768849715.569002038184.0534324964-3.855070179560.1939616680974.37503908238-3.676741178833.8158437507413.05664488539.7413188101-14.3749679379
73.98424612206-2.19904755099-3.433940636531.135759337931.981290737133.44799864443.09762396286-1.682801063174.05778962417-6.752349963727.139804250610.8354176849325.453265710560.415940498152-9.798084716632.56319625927-1.680191672230.2427777638654.137206022721.174486962927.283322841640.2966040194814.3035400048-15.0915407846
80.0397177342291-0.483966533903-0.2493137517696.938631832617.057690389657.310730338830.8775503100366.191399281953.883422504470.439892566431-0.343490652801-7.497767292832.768181296351.97273434971-0.7656972247653.735985332741.017056711451.817155855695.31599145904-1.112673400915.64190982368-6.7653976982423.6255680764-1.8766335896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 101 through 108)CA101 - 108
2X-RAY DIFFRACTION2(chain 'A' and resid 101 through 121)AB101 - 121
3X-RAY DIFFRACTION3(chain 'Y' and resid 101 through 110)YC101 - 110
4X-RAY DIFFRACTION4(chain 'X' and resid 101 through 104)XD101 - 104
5X-RAY DIFFRACTION5(chain 'X' and resid 105 through 110)XD105 - 110
6X-RAY DIFFRACTION6(chain 'B' and resid 101 through 104)BE101 - 104
7X-RAY DIFFRACTION7(chain 'B' and resid 105 through 107)BF105 - 107
8X-RAY DIFFRACTION8(chain 'D' and resid 109 through 114)DG109 - 114

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