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- PDB-7spl: [2T3] Self-assembling 3D DNA triangle with three inter-junction b... -

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Basic information

Entry
Database: PDB / ID: 7spl
Title[2T3] Self-assembling 3D DNA triangle with three inter-junction base pairs containing the L1 junction and a zero-linked center strand
Components
  • DNA (5'-D(*GP*AP*C)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*CP*C)-3')
  • DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*TP*AP*CP*AP*GP*GP*CP*TP*GP*C)-3')
KeywordsDNA / Tensegrity triangle / DNA nanotechnology / nanomaterials / linking number
Function / homology2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.09 Å
AuthorsVecchioni, S. / Lu, B. / Sha, R. / Ohayon, Y.P. / Seeman, N.C.
Funding support United States, 6items
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 United States
National Science Foundation (NSF, United States)DMR-1420073 United States
National Aeronautic Space Administration (NASA, United States)2020 NASA Center Innovation Fund United States
Citation
Journal: Small / Year: 2023
Title: The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles.
Authors: Vecchioni, S. / Lu, B. / Janowski, J. / Woloszyn, K. / Jonoska, N. / Seeman, N.C. / Mao, C. / Ohayon, Y.P. / Sha, R.
#1: Journal: To Be Published
Title: Mirror Nanomaterials: Self-Assembly of Left-Handed, Anti-Tensegrity DNA Triangles
Authors: Vecchioni, S. / Janowski, J. / Lu, B. / Ohayon, Y.P. / Sha, R. / Woloszyn, K. / Mao, C. / Seeman, N.C.
History
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 5, 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(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*CP*C)-3')
C: DNA (5'-D(P*GP*TP*AP*CP*AP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1035
Polymers12,7954
Non-polymers3071
Water00
1
A: DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*CP*C)-3')
C: DNA (5'-D(P*GP*TP*AP*CP*AP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*GP*AP*C)-3')
hetero molecules

A: DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*CP*C)-3')
C: DNA (5'-D(P*GP*TP*AP*CP*AP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*GP*AP*C)-3')
hetero molecules

A: DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*CP*C)-3')
C: DNA (5'-D(P*GP*TP*AP*CP*AP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,30815
Polymers38,38612
Non-polymers9223
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)87.841, 87.841, 140.534
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
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

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


Mass: 5506.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*CP*C)-3')


Mass: 3324.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*AP*CP*AP*GP*GP*CP*TP*GP*C)-3')


Mass: 3118.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*AP*C)-3')


Mass: 846.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-DC / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P / Comment: dCMP*YM
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: 8.41 Å3/Da / Density % sol: 84.92 % / Description: Rhombohedral
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / PH range: 7.8
Temp details: from 338K to 293K at 0.4K/hr; from 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: 6.033→66.9 Å / Num. obs: 765 / % possible obs: 83.2 % / Redundancy: 9.9 % / Biso Wilson estimate: 624.37 Å2 / CC1/2: 0.995 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID% possible all
6.033-7.2641910.039155.2
10.615-66.91920.9951100

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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: 6.09→36.72 Å / SU ML: 0.7037 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 56.6329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3348 30 5.06 %
Rwork0.2341 563 -
obs0.236 593 61.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 847.5 Å2
Refinement stepCycle: LAST / Resolution: 6.09→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 839 19 0 858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006958
X-RAY DIFFRACTIONf_angle_d1.30121467
X-RAY DIFFRACTIONf_chiral_restr0.1625167
X-RAY DIFFRACTIONf_plane_restr0.00542
X-RAY DIFFRACTIONf_dihedral_angle_d40.2051404
LS refinement shellResolution: 6.09→36.72 Å
RfactorNum. reflection% reflection
Rfree0.3348 30 -
Rwork0.2341 563 -
obs--61.07 %
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)
13.660965561592.1575853923-0.1856376980550.41223380841-0.0874374393511-0.01383259132571.0888854560.818279848783-0.8954413716620.5229587176760.4474997086269.09301373046-0.6342436791521.737874361558.672707076168.524661927-0.358018327743-1.2977779740812.79363771994.0560036280615.813706857-35.3368.7246.553
2-0.08545669920730.0278886845561-0.0553839541250.11217893301-0.06457006363610.0481007112931-3.61975857143-2.079499565464.37194043603-1.47379768864-3.76896791082-0.808271679952-5.44355293080.45151041272-16.840329573212.6783064684-1.696165860923.458192272449.35239085683-0.2505940937219.1703660111-36.398.314-11.47
30.112037616595-0.0528271281165-0.0315540991168-0.053017469417-0.0924951823857-0.0815151392089-5.328066576022.121931524970.9564929528535.58032610371-4.518472658030.7493852435434.74579495154.97842247774-29.2730660689.04371340741-0.712218318821-0.8106900741999.85176476201-1.1563228867714.7938986666-31.21511.03515.529
40.101105693588-0.184602030922-0.040384713710.4799590750470.128888041910.0183299867058-1.110152903660.3820913117731.13216357810.7601497597070.0565563998184-0.765608021518-1.323495223060.630484777901-1.086768355629.854154850450.3211508758913.7325878190213.6687956012-5.6413165189723.450718996-39.76321.1674.873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:19 )A1 - 19
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:10 )B1 - 10
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:10 )C1 - 10
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:3 )D1 - 3

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