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- PDB-8cs2: [(1AP)G/TC] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle -

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Basic information

Entry
Database: PDB / ID: 8cs2
Title[(1AP)G/TC] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle
Components
  • DNA (5'-D(*(1AP)P*GP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-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: 6 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(*(1AP)P*GP*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(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)12,8124
Polymers12,8124
Non-polymers00
Water00
1
A: DNA (5'-D(*(1AP)P*GP*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(*TP*CP*TP*GP*AP*TP*GP*T)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)38,43712
Polymers38,43712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)123.973, 123.973, 64.153
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

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Components

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


Mass: 6472.201 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(*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)
Has ligand of interestY

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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

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 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→61.99 Å / Num. obs: 1198 / % possible obs: 89.8 % / Redundancy: 19.5 % / Biso Wilson estimate: 191.51 Å2 / CC1/2: 1 / Net I/σ(I): 11.6
Reflection shellResolution: 6→6.75 Å / Num. unique obs: 200 / CC1/2: 0.117

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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: 6→41.17 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1997 58 5.12 %
Rwork0.1114 1075 -
obs0.1149 1133 76.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 627.06 Å2
Refinement stepCycle: LAST / Resolution: 6→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 856 0 0 856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221957
X-RAY DIFFRACTIONf_angle_d1.91811469
X-RAY DIFFRACTIONf_chiral_restr0.1133166
X-RAY DIFFRACTIONf_plane_restr0.012142
X-RAY DIFFRACTIONf_dihedral_angle_d38.5248400
LS refinement shellResolution: 6→41.17 Å
RfactorNum. reflection% reflection
Rfree0.1997 58 -
Rwork0.1114 1075 -
obs--76.35 %
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)
11.388683224410.135638923615-1.20063252371.494893878882.463712395932.92391578793-1.092720664940.3409889762981.92221755016-2.012664301312.831684484224.708827989150.312621507983-1.257424839940.001227621610546.98817669204-0.08673782041560.117426809437.043020950260.5123800610736.0050477953649.9485452656-25.4371264828-13.7896613143
2-0.03774049493320.0413092948495-0.2041794652380.1934925471280.1161901348630.02101799622750.0174184235097-2.622756957070.41359061327-0.34139399857-0.566511639342-2.59827903255-1.898409883460.3935558419520.008271341839955.864018290830.7170979246610.6890806965777.57702496261-0.1932705687888.6796142871349.9934563944-28.7826474908-11.4694449384
30.851870648924-1.123272729680.7340210109082.41088759839-1.574288917481.116899802655.346064234763.56752500981-0.6216604222870.492278532051-0.8059700586523.270340915112.68172624783-5.27709402517-0.0278989001537.78084772345-0.16938374346-0.7193788499389.252525161190.2250087767068.1055530129756.793236651-12.5340600865-24.719057546
40.9080629330530.888119882380.8846064884621.10160146490.5818120605910.6235087760352.516768790534.47146428858-7.545229818522.120258893096.1951971249311.82039136593.47580521005-0.1617687364110.5960035396976.8489218485-0.409251999536-0.8398155319948.328106886931.013434655696.6641182829438.7648484866-46.05226950740.266484078335
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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