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- PDB-7u3s: [2T7+21] Self-assembling tensegrity triangle with two turns of DN... -

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Basic information

Entry
Database: PDB / ID: 7u3s
Title[2T7+21] Self-assembling tensegrity triangle with two turns of DNA and the sticky end addition of a two-turn linker per axis with R3 symmetry
Components
  • DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*AP*G)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*CP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')
  • DNA (5'-D(P*TP*CP*TP*GP*AP*TP*GP*T)-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: 9.5 Å
AuthorsWoloszyn, K. / Vecchioni, S. / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,6846
Polymers25,6846
Non-polymers00
Water00
1
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
C: DNA (5'-D(P*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
X: DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*AP*G)-3')
Y: DNA (5'-D(P*TP*CP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)77,05118
Polymers77,05118
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)212.728, 212.728, 174.799
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 , 6 types, 6 molecules BCADXY

#1: DNA chain DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')


Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*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)
#3: DNA chain DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6457.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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)
#5: DNA chain DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*AP*G)-3')


Mass: 6552.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*TP*CP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')


Mass: 6334.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 29.64 Å3/Da / Density % sol: 95.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM MOPS, 125 mM magnesium sulfate, sodium hydroxide
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: 9.11→81.491 Å / Num. obs: 1413 / % possible obs: 83 % / Redundancy: 10.9 % / Biso Wilson estimate: 878.08 Å2 / CC1/2: 0.999 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
9.11-10.63511.72010.0881
19.983-81.49111.32020.999199.5

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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: 9.5→37.01 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.3145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1895 53 3.94 %
Rwork0.186 1291 -
obs0.1861 1344 73.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 798.48 Å2
Refinement stepCycle: LAST / Resolution: 9.5→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1722 0 0 1722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091926
X-RAY DIFFRACTIONf_angle_d1.15292958
X-RAY DIFFRACTIONf_chiral_restr0.06336
X-RAY DIFFRACTIONf_plane_restr0.007284
X-RAY DIFFRACTIONf_dihedral_angle_d38.9045822
LS refinement shellResolution: 9.5→37.01 Å
RfactorNum. reflection% reflection
Rfree0.1895 53 -
Rwork0.186 1291 -
obs--73.28 %
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)
12.45166338185-1.818457750471.621631190521.76535007434-2.461950265424.904470301220.2495807892880.299820292067-0.06140757240863.841947958061.312988023172.30111378664.841741238252.05958559338-1.3464078682210.3876343883-3.37849686072-0.21152115920813.23102327951.564522748017.732817954724.7550090640713.3077167324-47.0526485291
25.216151788140.550019557672.865940230270.09421199394330.2367379340631.63235361707-2.550657870981.259513978731.95570569368-1.15368640389-1.530042093730.831710422439-1.471534021693.06414599269-13.479867720312.417511662-0.5062192674274.9659211701210.8602079901-1.746263998377.12993695016-12.978897800522.0278836485-33.1042863305
30.71058932711-0.293132059813-0.4804945020810.5027648047970.3497293777320.144247052073.73466151416-1.02844081243-2.63371150891-1.516705101622.047616119594.476449387661.62527713445-2.1868733063311.12466492119.56465533530.2911349582423.2436995687511.720015108-0.539417407368.512055972048.740386702812.8565621137-49.1266368402
40.04620360888470.205261613893-0.1644296097641.04200004433-1.004486611181.06337756842-0.63574798109-1.37486785848-2.680118305661.57475091363-0.00296259131782-3.057563048890.9471317934150.345942028118-2.4925042556314.2348694993-2.925087049192.0477279875514.0390430468-2.908551892385.3913242740221.77612477946.06726982196-59.3043062207
50.03989027622190.188872461513-0.1416429769550.05388908996690.09371598510390.0132100376281-1.07357757058-2.7040553684-0.804062413666-2.83790414248-0.8755586194031.801978396610.681154942978-1.57094298748-9.5211687831713.0896411954-1.692476102752.0292565013712.118923111-2.173871842613.0746610909-41.870698386545.1680996474-17.9364913619
60.3362963648770.1151343024150.1885840169180.295307225208-0.2815199899750.287510253703-0.9506985114821.08446682-0.0580736638273-0.622227917338-0.138422125457-3.229612932020.1072464959910.0952266374814-4.6680915423412.06721852670.6624679607433.2612546010715.4622961058-2.781185666428.60788297589-48.376462850649.7873650541-14.8059884788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 130 through 136)BA130 - 136
2X-RAY DIFFRACTION2(chain 'C' and resid 122 through 129)CB122 - 129
3X-RAY DIFFRACTION3(chain 'A' and resid 101 through 121)AC101 - 121
4X-RAY DIFFRACTION4(chain 'D' and resid 137 through 142)DD137 - 142
5X-RAY DIFFRACTION5(chain 'X' and resid 122 through 142)XE122 - 142
6X-RAY DIFFRACTION6(chain 'Y' and resid 101 through 121)YF101 - 121

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