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- PDB-8cs1: [GA/CT] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle -

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Basic information

Entry
Database: PDB / ID: 8cs1
Title[GA/CT] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle
Components
  • DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(*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*CP*CP*GP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
KeywordsDNA / tensegrity triangle / synthetic construct / self-assembly
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.56 Å
AuthorsLu, B. / Vecchioni, S. / Ohayon, Y.P. / Seeman, N.C. / Mao, C. / Sha, R.
Funding support United States, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CTS1120890 United States
National Science Foundation (NSF, United States)CCF-1117210 United States
National Science Foundation (NSF, United States)EFRI-1332411 United States
National Science Foundation (NSF, United States)CHE-1708776 United States
Office of Naval Research (ONR)N000141110729 United States
Office of Naval Research (ONR)N000140911118 United States
Department of Energy (DOE, United States)DESC0007991 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles.
Authors: Lu, B. / Woloszyn, K. / Ohayon, Y.P. / Yang, B. / Zhang, C. / Mao, C. / Seeman, N.C. / Vecchioni, S. / Sha, R.
History
DepositionMay 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Oct 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
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*T)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)38,39212
Polymers38,39212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)123.316, 123.316, 57.154
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

#1: DNA chain DNA (5'-D(*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)
#2: 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)
#3: 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)
#4: DNA chain DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*T)-3')


Mass: 2432.614 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: 9.8 Å3/Da / Density % sol: 87.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.83 M ammonium sulfate, 120 mM Tris, 120 mM Acetic Acid, 6 mM EDTA
Temp details: 338-293 at 0.4/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 S 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: 4.56→20.01 Å / Num. obs: 2373 / % possible obs: 90.4 % / Redundancy: 20.3 % / Biso Wilson estimate: 329.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 4.56→4.9 Å / Num. unique obs: 200 / CC1/2: 0.551

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R96

7r96


Resolution: 4.56→20.01 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.1811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2206 141 5.95 %
Rwork0.214 2230 -
obs0.2144 2371 81.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 337.2 Å2
Refinement stepCycle: LAST / Resolution: 4.56→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166956
X-RAY DIFFRACTIONf_angle_d1.63191467
X-RAY DIFFRACTIONf_chiral_restr0.0966166
X-RAY DIFFRACTIONf_plane_restr0.009942
X-RAY DIFFRACTIONf_dihedral_angle_d40.7769406
LS refinement shellResolution: 4.56→20.01 Å
RfactorNum. reflection% reflection
Rfree0.2206 141 -
Rwork0.214 2230 -
obs--81.96 %
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)
15.47540670495-0.845421874121.169783658660.1282240128310.5298295989991.626687676352.300718455270.7937010986630.9565450618943.44723229507-2.35045465909-0.2177145352022.417709065751.86622112973-0.4418727269713.86079717667-0.223067689638-0.215896704963.51502764979-0.3479798808062.40933478608-46.661259576230.095351438316.3084032502
20.321189829129-0.3759780591470.164013918040.414503739732-0.2604677066570.1334570313152.044141125160.822936681839-0.3539594223841.80030203971.85138091459-2.050368576350.05555320831580.884919861920.03728271362812.8503465990.282999040692-0.2013345341862.70728322521-0.8101846461712.81978658323-49.557730880428.773540066214.3358789467
30.8862746782090.2271490062970.3769053877551.44771289231.921020922282.541849898562.000452439241.162879968920.7617997383891.743685979932.170261780531.7818932803-0.961087284624-2.984104639511.114141530654.310700061290.2736088540110.3670036587862.897731489960.8760302054823.30783580544-38.2978636442.276320839727.1948035499
45.219783482143.39628514923.100910281842.005273049353.116386017122.022232330180.9126897324940.400336054483-2.27586942349-4.784626128844.781693185741.9669879723-0.295235713149-1.339520582454.4623361135.25569378951-1.32343248344-3.159577510731.17472814799-1.849800036163.39506006827-59.242249616310.82933291522.60629583341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 101 through 121)AA101 - 121
2X-RAY DIFFRACTION2(chain 'B' and resid 119 through 125)BB119 - 125
3X-RAY DIFFRACTION3(chain 'C' and resid 209 through 214)CC209 - 214
4X-RAY DIFFRACTION4(chain 'D' and resid 201 through 208)DD201 - 208

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