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- PDB-8sju: [4T17] Self-assembling right-handed four-turn tensegrity triangle... -

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Basic information

Entry
Database: PDB / ID: 8sju
Title[4T17] Self-assembling right-handed four-turn tensegrity triangle with 17 interjunction base pairs and R3 symmetry
Components
  • DNA (25-MER)
  • DNA (5'-D(*GP*AP*AP*AP*AP*AP*CP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
  • DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
  • DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*CP*TP*CP*AP*AP*AP*A)-3')
KeywordsDNA / Tensegrity triangle / DNA nanotechnology / nanomaterials
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.14 Å
AuthorsJanowski, J. / Vecchioni, S. / Sha, R. / Ohayon, Y.P.
Funding support United States, France, 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 France
National Science Foundation (NSF, United States)DMR-1420073 United States
National Aeronautics and Space Administration (NASA, United States)2020 NASA Center Innovation Fund United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Engineering tertiary chirality in helical biopolymers.
Authors: Janowski, J. / Pham, V.A.B. / Vecchioni, S. / Woloszyn, K. / Lu, B. / Zou, Y. / Erkalo, B. / Perren, L. / Rueb, J. / Madnick, J. / Mao, C. / Saito, M. / Ohayon, Y.P. / Jonoska, N. / Sha, R.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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*AP*AP*AP*AP*CP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
C: DNA (25-MER)
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*CP*TP*CP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)25,7704
Polymers25,7704
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*AP*AP*AP*AP*CP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
C: DNA (25-MER)
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*CP*TP*CP*AP*AP*AP*A)-3')

A: DNA (5'-D(*GP*AP*AP*AP*AP*AP*CP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
C: DNA (25-MER)
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*CP*TP*CP*AP*AP*AP*A)-3')

A: DNA (5'-D(*GP*AP*AP*AP*AP*AP*CP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
C: DNA (25-MER)
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*CP*TP*CP*AP*AP*AP*A)-3')


  • defined by author
  • Evidence: native gel electrophoresis
  • 77.3 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)77,30912
Polymers77,30912
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)224.532, 224.532, 126.522
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

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


Mass: 7340.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')


Mass: 5187.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (25-MER)


Mass: 7716.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*CP*TP*CP*AP*AP*AP*A)-3')


Mass: 5524.605 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: 23.82 Å3/Da / Density % sol: 94.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338K-293K at 0.4K/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: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 6.988→77.092 Å / Num. obs: 2501 / % possible obs: 84.6 % / Redundancy: 10.7 % / Biso Wilson estimate: 407.84 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-IDMean I/σ(I) obs% possible all
6.988-7.6911.11890.2761
18.847-77.09210.51900.99512098.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W6W

5w6w


Resolution: 7.14→37.17 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.2202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1774 117 4.87 %
Rwork0.1106 2286 -
obs0.1126 2403 68.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 912.78 Å2
Refinement stepCycle: LAST / Resolution: 7.14→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1716 0 0 1716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041922
X-RAY DIFFRACTIONf_angle_d0.60862958
X-RAY DIFFRACTIONf_chiral_restr0.0288334
X-RAY DIFFRACTIONf_plane_restr0.00484
X-RAY DIFFRACTIONf_dihedral_angle_d35.6523826
LS refinement shellResolution: 7.14→37.17 Å
RfactorNum. reflection% reflection
Rfree0.1774 117 -
Rwork0.1106 2286 -
obs--68.15 %
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)
17.06422680230.655400625757-5.829876391961.05971135235-2.194767786063.296877457842.40789421707-1.50395326402-0.3473226970485.247478159881.448638633661.224389964235.51205865223-1.5104136347511.512325704713.87173461350.333118733748-4.664557753426.00809533723.488716835969.40439025002-20.8079061184-35.491023887922.3117447972
28.639992946880.772805349029-3.380268833260.671726246276-0.5655640341171.49740721548-3.48175431575-1.14839246151-2.238555219422.888754359682.50203767617-2.51564863948-1.857755132284.7178939236-4.3856282496811.8418218776-2.61588942316-7.904658011319.53473105088-1.0684042027710.3827290859-13.7913075583-33.8618252894-0.293095748026
32.014616193350.531517215729-2.29198958234-0.579444253514-0.04912331982242.14923427834-0.8331628182014.17438818417-2.292105507188.207745591310.3075568436967.54300509095-1.251228861731.03857243498-0.57933184353711.6142932846-1.881934962571.180894881828.466008490280.44530188590310.5208306432-8.94469906986-18.72063514669.40478350518
4-1.308129997560.208418158722.619847021361.71334930667-3.558493567454.2926743348-6.264517266695.71749263378-7.427669109141.304925218232.480325225352.74234419648-1.75868527495-3.29011431363-1.418162446828.18775329736-2.47687750444-0.15480885980611.1527313648-0.8710290518229.70536802339-23.286425023-45.64135656812.1827830926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'D' and resid 101 through 118)DD101 - 118
2X-RAY DIFFRACTION2(chain 'A' and resid 101 through 124)AA101 - 124
3X-RAY DIFFRACTION3(chain 'B' and resid 101 through 117)BB101 - 117
4X-RAY DIFFRACTION4(chain 'C' and resid 101 through 125)CC101 - 125

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